{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mySpecie='Homo_sapiens'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "import glob\n",
    "import gzip\n",
    "\n",
    "\n",
    "#snp_out_dir='/nrnb/users/btsui/Data/tcga_extracted_lgg_snp/'\n",
    "#/nrnb/users/btsui/Data/all_seq/snp/\n",
    "preprocessed_vcf_dir='/nrnb/users/btsui/Data/all_seq/snp/'\n",
    "\n",
    "inFnames=pd.Series(os.listdir(preprocessed_vcf_dir))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "outDir='/cellar/users/btsui/all_seq_snp/'+mySpecie+'.pickle'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/cellar/users/btsui/all_seq_snp/Homo_sapiens.pickle'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "outDir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "#vcfDirs=glob.glob('/nrnb/users/btsui/Data/tcga_orig_vcf/**/*.vcf$')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 183,
   "metadata": {},
   "outputs": [],
   "source": [
    "vcfDirs=glob.glob('/nrnb/users/btsui/Data/tcga_orig_vcf/**/*.vcf*')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#len(vcfDirs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 185,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tqdm import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
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      " 91%|█████████ | 1922/2119 [1:22:05<08:24,  2.56s/it]\u001b[A\n",
      " 91%|█████████ | 1923/2119 [1:22:08<08:22,  2.56s/it]\u001b[A\n",
      " 91%|█████████ | 1925/2119 [1:22:15<08:17,  2.56s/it]\u001b[A\n",
      " 91%|█████████ | 1927/2119 [1:22:26<08:12,  2.57s/it]\u001b[A\n",
      " 91%|█████████ | 1928/2119 [1:22:30<08:10,  2.57s/it]\u001b[A\n",
      " 91%|█████████ | 1929/2119 [1:22:41<08:08,  2.57s/it]\u001b[A\n",
      " 91%|█████████ | 1930/2119 [1:22:50<08:06,  2.58s/it]\u001b[A\n",
      " 91%|█████████ | 1931/2119 [1:23:01<08:04,  2.58s/it]\u001b[A\n",
      " 91%|█████████ | 1932/2119 [1:23:14<08:03,  2.58s/it]\u001b[A\n",
      " 91%|█████████ | 1933/2119 [1:23:19<08:01,  2.59s/it]\u001b[A\n",
      " 91%|█████████▏| 1934/2119 [1:23:20<07:58,  2.59s/it]\u001b[A\n",
      " 91%|█████████▏| 1935/2119 [1:23:20<07:55,  2.58s/it]\u001b[A\n",
      " 91%|█████████▏| 1936/2119 [1:23:27<07:53,  2.59s/it]\u001b[A\n",
      " 91%|█████████▏| 1937/2119 [1:23:29<07:50,  2.59s/it]\u001b[A\n",
      " 91%|█████████▏| 1938/2119 [1:23:38<07:48,  2.59s/it]\u001b[A\n",
      " 92%|█████████▏| 1939/2119 [1:23:38<07:45,  2.59s/it]\u001b[A\n",
      " 92%|█████████▏| 1940/2119 [1:23:38<07:43,  2.59s/it]\u001b[A\n",
      " 92%|█████████▏| 1941/2119 [1:23:49<07:41,  2.59s/it]\u001b[A\n",
      " 92%|█████████▏| 1942/2119 [1:23:49<07:38,  2.59s/it]\u001b[A\n",
      " 92%|█████████▏| 1943/2119 [1:24:02<07:36,  2.60s/it]\u001b[A\n",
      " 92%|█████████▏| 1944/2119 [1:24:14<07:35,  2.60s/it]\u001b[A\n",
      " 92%|█████████▏| 1945/2119 [1:24:17<07:32,  2.60s/it]\u001b[A\n",
      " 92%|█████████▏| 1947/2119 [1:24:21<07:27,  2.60s/it]\u001b[A\n",
      " 92%|█████████▏| 1948/2119 [1:24:22<07:24,  2.60s/it]\u001b[A\n",
      " 92%|█████████▏| 1949/2119 [1:24:36<07:22,  2.60s/it]\u001b[A"
     ]
    }
   ],
   "source": [
    "myL=[]\n",
    "for vcfDir in tqdm(vcfDirs):\n",
    "    myL.append(pd.read_csv(vcfDir,comment='#',header=None,sep='\\s+'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 201,
   "metadata": {},
   "outputs": [],
   "source": [
    "meregdDf=pd.concat(myL,axis=0,keys=vcfDirs,names=['fdir'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 202,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2119"
      ]
     },
     "execution_count": 202,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(myL)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 204,
   "metadata": {},
   "outputs": [],
   "source": [
    "meregdDf.to_pickle(outDir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "### analyze the allelic fraction against the primary tumors for somatic mutation calling?\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 209,
   "metadata": {},
   "outputs": [],
   "source": [
    "#!ls -lath ./TCGA_VCF.pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "asdasdasd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#!gunzip -c /nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz | head -n 23"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "scrolled": true
   },
   "source": [
    "\n",
    "!rm head.txt\n",
    "#MuSE_call_1\n",
    "\"\"\"\n",
    "with gzip.open('file.txt.gz', 'rb') as f:\n",
    "    file_content = f.read()\n",
    "\"\"\"\n",
    "fL=[]\n",
    "for i,vcfDir in enumerate(tqdm(vcfDirs)):\n",
    "    \n",
    "    with gzip.open(vcfDir, 'r') as f:\n",
    "        #.decode('ascii')\n",
    "        file_content = f.read().decode('ascii')\n",
    "\n",
    "    #str(file_content)\n",
    "    #print ( ('MuSE'  in file_content))\n",
    "    if not ('MuSE'  in file_content):\n",
    "        print (vcfDir)\n",
    "        os.system('echo \"{}\\n\" >>head.txt'.format(vcfDir))\n",
    "        os.system('gunzip -c {} | head -\n",
    "                  n 20 >>head.txt'.format(vcfDir))\n",
    "\n",
    "        os.system('echo \"\\n\" >> head.txt'.format(vcfDir))\n",
    "    fL.append(vcfDir)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "metadata": {},
   "outputs": [],
   "source": [
    "#lgg_rest_meta_df=pd.read_pickle('lgg_rest_meta.pickle')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 205,
   "metadata": {},
   "outputs": [],
   "source": [
    "#lgg_rest_meta_df.groupby('var_pipeline').first()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 206,
   "metadata": {},
   "outputs": [],
   "source": [
    "#529 files having all \n",
    "#'varscan_dr', 'muse', 'mutect', 'somaticsniper'\n",
    "#lgg_rest_meta_df.var_pipeline.value_counts().index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 207,
   "metadata": {},
   "outputs": [],
   "source": [
    "#lgg_rest_meta_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 167,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([], dtype=object)"
      ]
     },
     "execution_count": 167,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lgg_rest_meta_df['submitter_id'][~lgg_rest_meta_df['submitter_id'].str.contains('varscan_dr|somaticsniper|mutect|muse')].values#.str.split('_').str[-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 153,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/99690673-b98b-496c-bf5e-e08d3b3dc545/99690673-b98b-496c-bf5e-e08d3b3dc545.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job127557346_index_O09uzk/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1020217\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,2,0:33:36:0:26:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,0,0,2:33:36:33:33:60:60:2:16\r\n",
      "chr1\t1022591\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:9:0,9,0,0:0,0,9,0:54:60:0:33:52:52:0:.\t0/1:0/1:15:0,10,0,5:5,0,10,0:53:60:53:32,33:54:60,52:2:37\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c48297db-2dcd-4216-9033-f9bdbe433775/c48297db-2dcd-4216-9033-f9bdbe433775.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/dbfb00be-ed30-402f-bb2e-19e7d0ec340f/dbfb00be-ed30-402f-bb2e-19e7d0ec340f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
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      "/nrnb/users/btsui/Data/tcga_orig_vcf/4aa94453-1f1c-4120-864e-6b018f10704e/4aa94453-1f1c-4120-864e-6b018f10704e.vcf.gz\r\n",
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      "/nrnb/users/btsui/Data/tcga_orig_vcf/eef4b992-9147-45d9-9530-eaf2fedb2015/eef4b992-9147-45d9-9530-eaf2fedb2015.vcf.gz\r\n",
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      "/nrnb/users/btsui/Data/tcga_orig_vcf/7788aef6-5cae-47e7-ae87-9ebba4e9facb/7788aef6-5cae-47e7-ae87-9ebba4e9facb.vcf.gz\r\n",
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      "/nrnb/users/btsui/Data/tcga_orig_vcf/2e7db8f4-043d-4ec5-ad72-1f5f60cb9d5f/2e7db8f4-043d-4ec5-ad72-1f5f60cb9d5f.vcf.gz\r\n",
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      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/fd259142-5e82-4127-8bff-e611df8be734/fd259142-5e82-4127-8bff-e611df8be734.vcf.gz\r\n",
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      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/21f60c50-d463-422c-a5dd-b3b19bcaeab3/21f60c50-d463-422c-a5dd-b3b19bcaeab3.vcf.gz\r\n",
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      "/nrnb/users/btsui/Data/tcga_orig_vcf/44125418-c4b3-4c2a-9019-d88493a7116b/44125418-c4b3-4c2a-9019-d88493a7116b.vcf.gz\r\n",
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      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4d26f14f-16e1-4ec0-a8b4-fbc83957493a/4d26f14f-16e1-4ec0-a8b4-fbc83957493a.vcf.gz\r\n",
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      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t187497\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:132:72,36,20,4:24,0,108,0:52:120:0:29:29:31:0:.\t0/1:0/1:104:45,33,16,10:26,0,78,0:113:120:113:34,30:33:29,35:2:35\r\n",
      "chr1\t908209\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:20:0:35:60:60:0:.\t0/1:0/1:8:4,2,1,1:2,0,6,0:13:20:13:32,35:60:60,60:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f89f8da-d257-460e-bde6-798804da6a43/6f89f8da-d257-460e-bde6-798804da6a43.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/59e35df7-42dc-47d0-99e5-71167e225c9f/59e35df7-42dc-47d0-99e5-71167e225c9f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a35f0b8d-b832-479c-8547-f6f18b16dc7f/a35f0b8d-b832-479c-8547-f6f18b16dc7f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/41b6375b-42a1-4d1c-afaf-5063664265d6/41b6375b-42a1-4d1c-afaf-5063664265d6.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/1f001f73-d30e-4363-9fee-509fc0c0872c/1f001f73-d30e-4363-9fee-509fc0c0872c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8ad8ebe1-4091-4486-a98f-74568b1acacb/8ad8ebe1-4091-4486-a98f-74568b1acacb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/90902bbe-e9db-4ac3-8762-c65eb343a22d/90902bbe-e9db-4ac3-8762-c65eb343a22d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job407592064_index_Coi4O2/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t873857\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:88:48,23,11,6:0,71,16,0:38:69:0:32:33:36:0:.\t0/1:0/1:142:65,37,29,11:0,102,39,1:62:69:62:31,32:30:34,21:2:21\r\n",
      "chr1\t971419\t.\tA\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:2,0,0,0:31:23:0:16:60:60:0:.\t0/1:0/1:7:1,4,1,1:5,0,0,2:16:23:16:27,32:60:60,60:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/15888361-3b65-4696-813c-bd62f1b4391b/15888361-3b65-4696-813c-bd62f1b4391b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5da2428b-21b3-4296-a3e7-a58dfdb35f89/5da2428b-21b3-4296-a3e7-a58dfdb35f89.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/513a7dd9-2f05-437e-bfd4-ab96d9ce2721/513a7dd9-2f05-437e-bfd4-ab96d9ce2721.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/1717b93f-b3bb-432f-9829-892633593aed/1717b93f-b3bb-432f-9829-892633593aed.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160310\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job399196293_index_uWI20c/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t932716\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:3,1,0,0:0,0,0,4:39:63:0:31:60:60:0:.\t0/1:0/1:5:2,0,1,2:0,3,0,2:18:63:54:34,32:60:60,60:2:22\r\n",
      "chr1\t1033565\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:36:0:31:60:60:0:.\t0/1:1/1:3:0,1,1,1:2,0,1,0:4:36:33:32:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6a8081c5-b750-4be0-a8e4-844a45646f3f/6a8081c5-b750-4be0-a8e4-844a45646f3f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/96ccc7ed-5e0b-4f7b-a92b-deab64c693e8/96ccc7ed-5e0b-4f7b-a92b-deab64c693e8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/7445e19e-fa2b-4605-ab81-32a7ab1ebf62/7445e19e-fa2b-4605-ab81-32a7ab1ebf62.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/628b61c5-50de-476b-a5a7-45c2a0d0cd89/628b61c5-50de-476b-a5a7-45c2a0d0cd89.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f55e03f4-9d54-4692-8850-da3040d6096d/f55e03f4-9d54-4692-8850-da3040d6096d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job198795809_index_BmNF8p/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t10560\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,2,0,0:33:38:0:34:30:30:0:.\t0/1:1/1:3:0,1,1,1:0,1,2,0:23:38:33:33:35:46:2:16\r\n",
      "chr1\t52096\t.\tA\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:2,0,0,0:33:24:0:33:36:36:0:.\t0/1:1/1:2:0,0,0,2:0,2,0,0:33:24:33:30:35:35:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/83ee90ad-12cf-42d4-bea7-d20924bb04fb/83ee90ad-12cf-42d4-bea7-d20924bb04fb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3fe98ee9-e85c-412c-befa-814a1eebf7ea/3fe98ee9-e85c-412c-befa-814a1eebf7ea.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4c38f26b-95c4-4dc9-9b97-1af9b04ebbcb/4c38f26b-95c4-4dc9-9b97-1af9b04ebbcb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e0db645d-7929-4b58-bee9-1edd47141ced/e0db645d-7929-4b58-bee9-1edd47141ced.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b936c5ba-97a7-4744-9bfb-88e1c3bfecf4/b936c5ba-97a7-4744-9bfb-88e1c3bfecf4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/95f3638c-1e6d-4a41-929a-c547a4716ff8/95f3638c-1e6d-4a41-929a-c547a4716ff8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job237679929_index_onB2G9/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t873857\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:90:56,22,8,4:0,78,12,0:90:17:0:32:32:33:0:.\t0/1:0/1:131:73,25,27,6:1,98,32,0:10:17:10:31,33:31:34,22:2:17\r\n",
      "chr1\t948721\t.\tA\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:17:0,17,0,0:17,0,0,0:78:41:0:30:60:60:0:.\t0/1:0/1:16:0,12,0,4:12,4,0,0:34:41:34:30,33:60:60,60:2:41\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/267961b2-e186-4bf6-a837-3b2ea2ff5b16/267961b2-e186-4bf6-a837-3b2ea2ff5b16.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/7c5e3042-559e-4ad3-bbfb-87b5a52b16c4/7c5e3042-559e-4ad3-bbfb-87b5a52b16c4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job389287182_index_i_AP3J/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t873857\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:164:80,56,19,9:0,136,28,0:86:134:0:32:27:28:0:.\t0/1:0/1:152:71,32,35,14:0,103,49,0:127:134:127:32,33:28:29,24:2:69\r\n",
      "chr1\t1182106\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:2,0,0,0:33:45:0:31:60:60:0:.\t0/1:1/1:3:0,0,3,0:0,0,3,0:36:45:36:29:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/936c32ab-ba7e-49a4-8026-0e9c5adb8f3a/936c32ab-ba7e-49a4-8026-0e9c5adb8f3a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/de2c4f4e-738f-47e2-bc66-a71f57518af4/de2c4f4e-738f-47e2-bc66-a71f57518af4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8cb7d577-57db-415e-b13a-08f689fd1b2b/8cb7d577-57db-415e-b13a-08f689fd1b2b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/844601ff-21db-4161-954b-5e1c50a4d5bc/844601ff-21db-4161-954b-5e1c50a4d5bc.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job55727519_index_NScfAF/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t966426\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:5,0,0,0:0,0,5,0:42:83:0:33:60:60:0:.\t0/1:0/1:9:4,0,5,0:0,5,4,0:58:83:76:34,35:60:60,60:2:25\r\n",
      "chr1\t1048922\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,0,2:33:38:0:34:60:60:0:.\t0/1:0/1:6:2,1,2,1:0,3,0,3:31:38:31:27,35:60:60,60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5c072661-b257-4bd4-aac5-1b44646f5e31/5c072661-b257-4bd4-aac5-1b44646f5e31.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5d98c68b-afb5-42d7-aae2-ec3e83ecf9c0/5d98c68b-afb5-42d7-aae2-ec3e83ecf9c0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d48ab309-44d0-44f0-99b2-d65b1cc89f23/d48ab309-44d0-44f0-99b2-d65b1cc89f23.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/300952f6-348f-402f-94a7-919dc99f43bd/300952f6-348f-402f-94a7-919dc99f43bd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/478b4f88-6e7c-4e76-a3f3-7824437c5ff1/478b4f88-6e7c-4e76-a3f3-7824437c5ff1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/86648923-2ea2-4825-9c93-c550d59a4d8e/86648923-2ea2-4825-9c93-c550d59a4d8e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job223417748_index_w7yvpr/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1184277\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:0,3,0,0:0,0,3,0:36:23:0:31:60:60:0:.\t0/1:0/1:4:0,2,0,2:0,2,2,0:16:23:16:29,31:60:60,60:2:18\r\n",
      "chr1\t1232848\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:3,2,0,0:0,5,0,0:42:21:0:27:60:60:0:.\t0/1:0/1:5:2,1,2,0:2,3,0,0:14:21:14:30,27:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/1eae65af-8a16-4d4d-a34c-9d8af925abf6/1eae65af-8a16-4d4d-a34c-9d8af925abf6.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e5fd1c95-e4c1-4ede-8940-cfcfce7a4e8e/e5fd1c95-e4c1-4ede-8940-cfcfce7a4e8e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job399155408_index_gMOHuw/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t182686\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:3,2,0,0:5,0,0,0:42:26:0:29:22:22:0:.\t0/1:0/1:8:3,2,3,0:5,0,3,0:19:26:19:33,29:44:48,37:2:22\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:212:85,102,11,14:24,0,187,1:203:32:0:31:52:56:0:.\t0/1:0/1:103:28,52,8,15:21,1,80,0:25:32:25:34,31:49:25,56:2:32\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5593f47b-56c8-4a27-bd31-3c749725a34f/5593f47b-56c8-4a27-bd31-3c749725a34f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c66f9910-c294-405f-828a-5f5591a5edda/c66f9910-c294-405f-828a-5f5591a5edda.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job187398651_index_J_rhlt/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t957428\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,4,0,0:39:22:0:33:60:60:0:.\t0/1:1/1:2:0,0,0,2:1,0,0,1:2:22:3:32:60:60:2:22\r\n",
      "chr1\t960326\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:41:0:33:60:60:0:.\t0/1:1/1:2:0,0,1,1:2,0,0,0:33:41:33:33:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/658e9cc6-2766-46dd-998d-d250a0626a02/658e9cc6-2766-46dd-998d-d250a0626a02.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0db3d19f-26f6-448e-818d-ff412e5812c1/0db3d19f-26f6-448e-818d-ff412e5812c1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job520016403_index_Y9RMcK/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1509162\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:28:22,3,2,1:0,0,25,3:38:61:0:28:32:32:0:.\t0/1:0/1:23:16,1,4,2:0,0,17,6:54:61:54:28,32:32:33,31:2:21\r\n",
      "chr1\t1522905\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:19:6,11,0,2:17,0,2,0:46:34:0:27:45:47:0:.\t0/1:0/1:29:4,16,1,8:20,0,9,0:27:34:27:30,26:43:51,26:2:28\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3eee1a32-6c75-4cbc-a585-4bfcdcf009a7/3eee1a32-6c75-4cbc-a585-4bfcdcf009a7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job796512207_index_O2cWNU/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183697\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:7:6,1,0,0:0,0,7,0:48:30:0:29:24:24:0:.\t0/1:0/1:12:8,0,4,0:4,0,8,0:23:30:23:32,33:24:26,23:2:27\r\n",
      "chr1\t975983\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,0,2,0:33:33:0:33:60:60:0:.\t0/1:1/1:3:1,0,1,1:2,0,1,0:9:33:33:31:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4c14381c-dafd-48d7-8350-8e06450bdae0/4c14381c-dafd-48d7-8350-8e06450bdae0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/75f89481-d732-4d74-b35c-8db8130066c2/75f89481-d732-4d74-b35c-8db8130066c2.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b03250cf-acea-4e98-b9e3-13796a3b5c12/b03250cf-acea-4e98-b9e3-13796a3b5c12.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0ba20775-e673-48fa-82bf-0caa78c666ec/0ba20775-e673-48fa-82bf-0caa78c666ec.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/9cde07f0-7fb3-459d-a6b6-a9af744696c7/9cde07f0-7fb3-459d-a6b6-a9af744696c7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6b606d7f-ad49-4e85-984e-ff191c1954e0/6b606d7f-ad49-4e85-984e-ff191c1954e0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a7b103a9-0532-4119-a027-f4acf3feb552/a7b103a9-0532-4119-a027-f4acf3feb552.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/cef7785c-6e73-4525-acb3-9f4bde134860/cef7785c-6e73-4525-acb3-9f4bde134860.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job159272406_index_NY1bjy/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t17020\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,0,2,0:33:30:0:32:23:23:0:.\t0/1:0/1:5:1,1,1,2:3,0,2,0:3:30:23:30,32:23:23,22:2:16\r\n",
      "chr1\t17495\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:6:0,6,0,0:0,6,0,0:45:25:0:34:38:38:0:.\t0/1:0/1:5:2,1,1,1:2,3,0,0:18:25:18:30,32:42:40,43:2:23\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/491a35ed-1e0b-47f8-9ef5-4e5b9d4d1e5b/491a35ed-1e0b-47f8-9ef5-4e5b9d4d1e5b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job73561579_index_ADlClh/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t782105\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:32:0:29:40:40:0:.\t0/1:0/1:5:0,3,0,2:2,3,0,0:25:32:25:36,29:43:45,41:2:24\r\n",
      "chr1\t874352\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:129:38,67,7,17:0,24,0,105:34:20:0:32:53:60:0:.\t0/1:0/1:119:33,65,8,13:0,21,0,98:13:20:13:35,32:55:29,60:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e376dee3-78ab-4d7f-b966-3022b8c3f2d9/e376dee3-78ab-4d7f-b966-3022b8c3f2d9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job641603666_index_KSV2Kg/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1519934\t.\tT\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:33:23:0:32:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,0,2,0:33:23:33:26:60:60:2:15\r\n",
      "chr1\t1519938\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:33:36:0:32:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,2,0,0:33:36:33:33:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8748b776-fbcd-4a3c-a9a1-cb1210c5b76b/8748b776-fbcd-4a3c-a9a1-cb1210c5b76b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job621196582_index_8qFTt7/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1054900\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,2,0,0:33:108:0:30:60:60:0:.\t0/1:0/1:10:1,3,2,4:0,4,0,6:43:108:88:27,31:60:60,60:2:16\r\n",
      "chr1\t1309863\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:31:0:22:60:60:0:.\t0/1:0/1:4:0,2,1,1:2,2,0,0:24:31:24:31,34:60:60,60:2:24\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/672abd81-388e-46c1-aaf1-4cd9f255886b/672abd81-388e-46c1-aaf1-4cd9f255886b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/19c3c1e7-7d6f-4785-bc6a-4a1ca4cd9467/19c3c1e7-7d6f-4785-bc6a-4a1ca4cd9467.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job241064353_index_xW2u4o/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t182686\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:12:9,2,1,0:11,0,1,0:35:20:0:34:34:33:0:.\t0/1:0/1:8:3,2,3,0:5,0,3,0:13:20:13:31,25:45:43,47:2:16\r\n",
      "chr1\t791542\t.\tC\tA,T\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/2:2/2:2:0,0,1,1:0,0,0,2:33:30:33:33:34:34:1:.\t0/1:0/1:4:2,0,1,1:2,2,0,0:1:30:17:28,29:27:29,26:2:29\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/865f6278-b0c5-42f6-93da-e755c2c1b201/865f6278-b0c5-42f6-93da-e755c2c1b201.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/fce0210e-956d-4ab2-9fa3-65e70987f92f/fce0210e-956d-4ab2-9fa3-65e70987f92f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job513825787_index_rqZz9C/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t874352\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:121:33,76,4,8:0,12,0,109:186:68:0:31:56:60:0:.\t0/1:0/1:89:16,49,14,10:1,23,0,65:61:68:61:33,32:49:19,60:2:68\r\n",
      "chr1\t1239942\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:6:4,2,0,0:0,0,6,0:45:29:0:29:60:60:0:.\t0/1:0/1:5:2,1,1,1:0,0,3,2:22:29:22:30,32:60:60,60:2:25\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/36f902f6-d75e-4a79-8436-e7ddbef56ca8/36f902f6-d75e-4a79-8436-e7ddbef56ca8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8fe4c94a-8da9-463d-becc-3afdf8db9380/8fe4c94a-8da9-463d-becc-3afdf8db9380.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job794909707_index_1u57l9/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t187497\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:168:89,57,14,8:22,0,146,0:106:55:0:30:34:35:0:.\t0/1:0/1:180:95,41,29,15:44,0,136,0:48:55:48:32,29:28:22,30:2:55\r\n",
      "chr1\t874352\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:100:33,53,2,12:0,14,0,86:93:26:0:32:55:60:0:.\t0/1:0/1:95:32,41,9,13:0,22,0,73:19:26:19:34,32:51:20,60:2:26\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e09ec1b5-ea2f-467c-8618-a55ec2366077/e09ec1b5-ea2f-467c-8618-a55ec2366077.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job533995896_index_n2NQt5/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t972251\t.\tA\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:46:26,7,1,12:33,12,1,0:34:28:0:29:60:60:0:.\t0/1:0/1:40:19,9,0,12:28,12,0,0:21:28:21:23,21:60:60,60:2:17\r\n",
      "chr1\t1041823\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:6:6,0,0,0:0,0,6,0:45:24:0:33:60:60:0:.\t0/1:0/1:9:5,1,2,1:0,3,6,0:17:24:17:25,36:56:60,53:2:23\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/551ed907-025d-44da-9671-175f805444e1/551ed907-025d-44da-9671-175f805444e1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/653008a2-2973-4b92-8e29-b8edd649070a/653008a2-2973-4b92-8e29-b8edd649070a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d8139160-ed8c-4ce2-89c8-43e14c6adf17/d8139160-ed8c-4ce2-89c8-43e14c6adf17.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6db236f3-607c-4365-8644-0db6c9ac02c9/6db236f3-607c-4365-8644-0db6c9ac02c9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f704b4d2-af43-409a-9f3f-4ddffc24cb39/f704b4d2-af43-409a-9f3f-4ddffc24cb39.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3e892792-7dca-45c0-a51c-48344984fb4b/3e892792-7dca-45c0-a51c-48344984fb4b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job895542495_index_cYXKk0/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t929839\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:2,1,0,0:0,0,3,0:36:56:0:28:60:60:0:.\t0/1:1/1:3:0,0,1,2:3,0,0,0:36:56:36:30:60:60:2:19\r\n",
      "chr1\t929903\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,2,0,0:33:56:0:30:60:60:0:.\t0/1:1/1:4:0,1,1,2:0,1,0,3:8:56:36:31:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f76e340a-ac87-4232-af4d-bff6991a2553/f76e340a-ac87-4232-af4d-bff6991a2553.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job11684446_index_TS5CZi/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:180:69,91,12,8:19,0,160,0:229:40:0:31:52:56:0:.\t0/1:0/1:110:35,50,8,17:25,0,85,0:33:40:33:31,31:48:23,56:2:40\r\n",
      "chr1\t874307\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:180:69,93,11,7:0,18,162,0:250:27:0:34:53:57:0:.\t0/1:0/1:111:35,51,8,17:0,25,86,0:20:27:20:28,33:50:23,58:2:27\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/50896ac5-d8be-4ec3-94ac-471fc8993e4c/50896ac5-d8be-4ec3-94ac-471fc8993e4c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job945451079_index_DtN3q8/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t803762\t.\tT\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,0,2:33:39:0:28:40:40:0:.\t0/1:1/1:3:0,0,2,1:3,0,0,0:36:39:36:32:23:23:2:16\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:148:54,78,10,6:15,0,132,0:185:40:0:29:51:54:0:.\t0/1:0/1:150:43,77,14,16:29,0,120,1:33:40:33:33,30:49:26,55:2:40\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d7c48f6b-25d8-4b8b-88bc-55c81e2a28e4/d7c48f6b-25d8-4b8b-88bc-55c81e2a28e4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/dfb93061-bbe2-4f27-85df-59c57cd10f89/dfb93061-bbe2-4f27-85df-59c57cd10f89.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0ea3b6ec-d3f1-45ef-b3f3-69a9e61f93fc/0ea3b6ec-d3f1-45ef-b3f3-69a9e61f93fc.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job359730471_index_yIVh8g/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1054900\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:1,2,0,0:0,3,0,0:36:33:0:29:60:60:0:.\t0/1:1/1:2:0,0,1,1:0,0,0,2:33:33:33:29:60:60:2:19\r\n",
      "chr1\t1388206\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:11:0,11,0,0:0,11,0,0:60:20:0:36:60:60:0:.\t0/1:0/1:5:0,3,0,2:0,3,0,2:13:20:13:31,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5a84908c-5aab-41aa-aca0-d1d666727417/5a84908c-5aab-41aa-aca0-d1d666727417.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bacb549a-5425-404c-995c-3faad7a20580/bacb549a-5425-404c-995c-3faad7a20580.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/ca98ebfe-d0e4-472d-9d8d-e65b5991f812/ca98ebfe-d0e4-472d-9d8d-e65b5991f812.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/7ca78c7e-aaaf-4f0b-91f3-a71281e9e750/7ca78c7e-aaaf-4f0b-91f3-a71281e9e750.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/784bf14d-2d2c-4199-a89b-0c4faa2c6e25/784bf14d-2d2c-4199-a89b-0c4faa2c6e25.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/020879e0-9ef5-40e4-89c9-409323e86d5a/020879e0-9ef5-40e4-89c9-409323e86d5a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/7f4b5061-66db-432f-8783-509f313da6f2/7f4b5061-66db-432f-8783-509f313da6f2.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/9ad50bf6-9fe0-4ad7-b26f-b6f52824ef9e/9ad50bf6-9fe0-4ad7-b26f-b6f52824ef9e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/eb19d1eb-3497-49c9-8619-245ad90737fb/eb19d1eb-3497-49c9-8619-245ad90737fb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/14c29283-a851-450b-bed3-da067a691dd0/14c29283-a851-450b-bed3-da067a691dd0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job54932884_index_ugZDi6/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14653\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:35:29,4,2,0:0,33,0,2:99:35:0:30:21:22:0:.\t0/1:0/1:24:11,5,7,1:0,16,0,8:28:35:28:32,31:22:23,22:2:35\r\n",
      "chr1\t873857\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:103:64,19,13,7:1,83,19,0:57:59:0:31:28:30:0:.\t0/1:0/1:62:28,18,11,5:0,46,16,0:52:59:52:32,35:30:33,22:2:40\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/05e477c2-9fa7-4d9a-8a98-6b7b805348f1/05e477c2-9fa7-4d9a-8a98-6b7b805348f1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job840590575_index_ei_zjq/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1237063\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,0,2,0:33:31:0:32:60:60:0:.\t0/1:1/1:3:0,1,1,1:0,0,1,2:3:31:27:30:60:60:2:16\r\n",
      "chr1\t1455337\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:2,0,0,0:33:29:0:27:60:60:0:.\t0/1:1/1:4:1,0,3,0:1,0,3,0:12:29:34:23:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0d4b0a89-7c06-48d6-9180-e69146c5b27c/0d4b0a89-7c06-48d6-9180-e69146c5b27c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c48a1c11-9d11-4d98-b1ae-0c600757746f/c48a1c11-9d11-4d98-b1ae-0c600757746f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job111296575_index_vxlJXR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1126128\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:3,0,0,0:0,0,3,0:10:22:0:2:5:5:0:.\t0/1:1/1:3:1,0,1,1:2,0,1,0:28:22:33:31:44:60:2:17\r\n",
      "chr1\t1296255\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:10:2,8,0,0:0,10,0,0:57:17:0:32:60:60:0:.\t0/1:0/1:9:0,7,1,1:2,7,0,0:10:17:10:32,32:60:60,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/ebcba6b5-6264-44cd-b8a9-386fe086d0cb/ebcba6b5-6264-44cd-b8a9-386fe086d0cb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d5bd22ef-14ec-4173-8141-f6df4426d71c/d5bd22ef-14ec-4173-8141-f6df4426d71c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job611462398_index_3UapdL/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:181:68,92,13,8:21,0,160,0:197:42:0:28:51:54:0:.\t0/1:0/1:146:44,67,14,21:34,1,111,0:35:42:35:32,27:45:18,53:2:42\r\n",
      "chr1\t874307\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:180:65,92,13,10:0,23,157,0:174:26:0:32:53:57:0:.\t0/1:0/1:138:44,59,14,21:0,35,103,0:19:26:19:27,31:46:19,56:2:26\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/628cee15-33c7-45ee-be4f-76c4e5a7233d/628cee15-33c7-45ee-be4f-76c4e5a7233d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6da7b2d9-7ee6-4f69-a565-463a9daf3208/6da7b2d9-7ee6-4f69-a565-463a9daf3208.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job567974803_index_WFGLEf/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:204:76,103,13,12:25,0,179,0:184:198:0:30:51:55:0:.\t0/1:0/1:251:56,94,49,52:101,0,150,0:191:198:191:33,30:41:21,55:2:167\r\n",
      "chr1\t874307\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:207:76,106,13,12:0,25,182,0:208:220:0:33:53:57:0:.\t0/1:0/1:249:53,92,50,54:0,102,145,2:214:220:214:30,33:42:20,58:2:191\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/72271fed-5d7d-426d-bfcd-0e83756b10c5/72271fed-5d7d-426d-bfcd-0e83756b10c5.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/50c31528-dd1a-437d-a40c-df1142ef7843/50c31528-dd1a-437d-a40c-df1142ef7843.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2e4b8567-bec1-48dd-a13e-4476421a9ed7/2e4b8567-bec1-48dd-a13e-4476421a9ed7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/45426b88-6b59-409a-a485-59eb5aed08ab/45426b88-6b59-409a-a485-59eb5aed08ab.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2bffdf56-3e6e-4720-89bb-64eb6d5527eb/2bffdf56-3e6e-4720-89bb-64eb6d5527eb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job613377736_index_dTt4i0/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1041370\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:6:5,1,0,0:0,0,6,0:45:34:0:34:60:60:0:.\t0/1:0/1:4:2,0,1,1:0,0,2,2:25:34:27:34,33:60:60,60:2:27\r\n",
      "chr1\t1213643\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:9:6,3,0,0:0,0,9,0:54:26:0:32:60:60:0:.\t0/1:0/1:7:5,0,1,1:0,0,5,2:19:26:19:27,33:60:60,60:2:26\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2ff8f3ab-cd0e-4409-bbfa-7199caf198d5/2ff8f3ab-cd0e-4409-bbfa-7199caf198d5.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e8ace314-76d3-4089-aa4e-12a497651b34/e8ace314-76d3-4089-aa4e-12a497651b34.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/fe28e2fe-eada-461a-ad82-a3b3038b21b9/fe28e2fe-eada-461a-ad82-a3b3038b21b9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0ec42270-dfde-4561-88db-854874c30030/0ec42270-dfde-4561-88db-854874c30030.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job450580921_index_8BSXHa/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14653\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:30:20,5,5,0:0,25,0,5:45:16:0:33:22:22:0:.\t0/1:0/1:16:9,3,3,1:0,12,0,4:9:16:9:32,34:23:23,23:2:16\r\n",
      "chr1\t1182895\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:19:12,7,0,0:0,19,0,0:84:16:0:34:60:60:0:.\t0/1:0/1:11:8,1,1,1:0,9,0,2:9:16:9:36,34:60:60,60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e7016f32-0703-4dd4-874d-cf41492e0275/e7016f32-0703-4dd4-874d-cf41492e0275.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160310\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job27850380_index__72vqN/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t877037\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:2,0,0,0:33:53:0:33:60:60:0:.\t0/1:0/1:7:1,1,4,1:2,0,5,0:15:53:46:31,33:34:60,24:2:16\r\n",
      "chr1\t877045\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,0,2,0:33:44:0:33:60:60:0:.\t0/1:0/1:6:1,1,3,1:4,0,2,0:21:44:37:31,33:39:29,60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a0cf7db2-fb3d-4811-b3d0-053c2d4d4fa2/a0cf7db2-fb3d-4811-b3d0-053c2d4d4fa2.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3d750d33-3567-4bea-bad5-a67c22ee6be6/3d750d33-3567-4bea-bad5-a67c22ee6be6.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job922796111_index_RDbJ4E/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t17556\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,2,0,0:33:35:0:33:34:34:0:.\t0/1:1/1:3:0,1,1,1:0,1,0,2:26:35:33:32:27:36:2:16\r\n",
      "chr1\t133194\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:2,2,0,0:0,4,0,0:39:18:0:35:51:51:0:.\t0/1:0/1:10:8,0,1,1:2,8,0,0:11:18:11:34,33:43:60,38:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/409a84e8-f202-4354-9561-262ef5ba3352/409a84e8-f202-4354-9561-262ef5ba3352.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/02d0d05a-7527-44d9-9715-fedf78ea7e19/02d0d05a-7527-44d9-9715-fedf78ea7e19.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job851047621_index_zRctpO/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t944350\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:0,2,0,0:0,2,0,0:33:35:0:27:60:60:0:.\t0/1:0/1:4:0,2,1,1:2,2,0,0:11:35:28:33,27:60:60,60:2:16\r\n",
      "chr1\t1068437\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:2,3,0,0:0,0,5,0:42:21:0:30:60:60:0:.\t0/1:1/1:3:1,0,1,1:2,0,1,0:15:21:29:25:60:60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/543408ab-1bb4-47f1-a59a-3dd5b0ea14d9/543408ab-1bb4-47f1-a59a-3dd5b0ea14d9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/742c1e15-01b9-471b-b01d-6198d48079a8/742c1e15-01b9-471b-b01d-6198d48079a8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0ce0240d-6a3e-46d8-a795-d2872fcfd46d/0ce0240d-6a3e-46d8-a795-d2872fcfd46d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2474fbd3-5e12-49f0-b596-6dc294ace8af/2474fbd3-5e12-49f0-b596-6dc294ace8af.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job879639388_index_ulBsRR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t835465\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:1,3,0,0:0,0,4,0:39:28:0:32:43:43:0:.\t0/1:1/1:2:0,0,1,1:2,0,0,0:33:28:33:31:27:27:2:21\r\n",
      "chr1\t971144\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:9,5,0,0:0,0,14,0:69:193:0:26:60:60:0:.\t0/1:0/1:26:7,6,8,5:13,0,13,0:185:193:186:32,31:60:60,60:2:52\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a7707f60-f9b9-4242-8b43-7ee28f31efa8/a7707f60-f9b9-4242-8b43-7ee28f31efa8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job356272531_index_jEU44c/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t13273\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:42:0:31:24:24:0:.\t0/1:1/1:5:1,1,2,1:0,3,2,0:3:42:36:32:27:32:2:16\r\n",
      "chr1\t14653\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:13:7,6,0,0:0,13,0,0:66:18:0:26:21:21:0:.\t0/1:0/1:13:8,1,4,0:0,9,0,4:11:18:11:32,34:22:22,23:2:18\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5e2c2661-7d51-48f8-a824-978fe1b9ecfd/5e2c2661-7d51-48f8-a824-978fe1b9ecfd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d2d7622c-97cd-4d0b-bdbe-9f9302d8ba70/d2d7622c-97cd-4d0b-bdbe-9f9302d8ba70.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job181350658_index_u0SrZu/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t186536\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,4,0,0:39:31:0:27:18:18:0:.\t0/1:1/1:6:0,2,0,4:0,2,0,4:13:31:37:33:19:21:2:21\r\n",
      "chr1\t1087713\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:33:31:0:30:60:60:0:.\t0/1:1/1:2:0,0,1,1:0,2,0,0:33:31:33:28:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b979479e-edaa-4ef8-955d-0378f9b52c0b/b979479e-edaa-4ef8-955d-0378f9b52c0b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3cdb5155-534c-4a57-bde1-9dcd225ee0e3/3cdb5155-534c-4a57-bde1-9dcd225ee0e3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/03541f9c-ece8-46a5-b060-4fbcbeae52ad/03541f9c-ece8-46a5-b060-4fbcbeae52ad.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job519632517_index_Aacmsh/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t942612\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:2,3,0,0:0,5,0,0:42:33:0:33:60:60:0:.\t0/1:1/1:3:0,1,1,1:0,1,0,2:5:33:31:31:60:60:2:24\r\n",
      "chr1\t1214147\t.\tA\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:24:11,13,0,0:24,0,0,0:99:24:0:33:60:60:0:.\t0/1:0/1:8:1,5,1,1:6,0,0,2:17:24:17:32,34:60:60,60:2:24\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d0e799b5-3c1f-4d6c-97d1-05a3fa421321/d0e799b5-3c1f-4d6c-97d1-05a3fa421321.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/257ef2a3-d03b-44a4-ba73-8fdffae58dd2/257ef2a3-d03b-44a4-ba73-8fdffae58dd2.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job672146980_index_zRFpMT/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14653\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:21:13,6,2,0:0,19,0,2:53:39:0:29:19:19:0:.\t0/1:0/1:21:10,4,6,1:0,14,0,7:32:39:32:29,31:17:14,22:2:34\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:195:72,103,10,10:20,0,175,0:216:69:0:30:51:54:0:.\t0/1:0/1:152:57,60,17,18:33,0,117,0:62:69:62:33,29:47:26,53:2:69\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/daf0b9d4-344b-4a7f-a806-708a60163d8a/daf0b9d4-344b-4a7f-a806-708a60163d8a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8186800e-cd84-40a8-aacd-4017db8b5c01/8186800e-cd84-40a8-aacd-4017db8b5c01.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/303d8054-5ea4-4330-9e2d-0870649b6b94/303d8054-5ea4-4330-9e2d-0870649b6b94.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6b3e88d4-72fe-4cf1-93af-0cb43849bcbc/6b3e88d4-72fe-4cf1-93af-0cb43849bcbc.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job877222183_index_vCjke9/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14653\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:20:10,9,1,0:0,19,0,1:64:18:0:27:18:17:0:.\t0/1:0/1:11:5,1,4,1:0,6,0,5:4:18:11:23,31:15:15,16:2:18\r\n",
      "chr1\t1042118\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:20:10,10,0,0:0,0,20,0:87:23:0:30:60:60:0:.\t0/1:0/1:6:1,3,1,1:0,0,4,2:16:23:16:33,30:60:60,60:2:23\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a99e4587-3414-4c10-a4ba-604bb0300bb0/a99e4587-3414-4c10-a4ba-604bb0300bb0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/68e55d82-f352-4f1d-8581-fe2d5a8dbd8f/68e55d82-f352-4f1d-8581-fe2d5a8dbd8f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3298901a-d3d1-47f2-a4fc-d516c5458caf/3298901a-d3d1-47f2-a4fc-d516c5458caf.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job771748187_index_Eol4pK/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1082764\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:4,0,0,0:0,0,0,4:39:33:0:26:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,2,0,0:33:33:33:32:60:60:2:22\r\n",
      "chr1\t1314344\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:16:9,7,0,0:0,0,16,0:75:19:0:33:60:60:0:.\t0/1:0/1:10:6,2,1,1:0,0,8,2:12:19:12:34,34:60:60,60:2:19\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/84590cda-2777-471b-badb-60bf023c75de/84590cda-2777-471b-badb-60bf023c75de.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4a9c2c7e-20bd-46e5-8362-3b40c01002ca/4a9c2c7e-20bd-46e5-8362-3b40c01002ca.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job166420704_index_YxtUa8/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t964905\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:52:0:35:60:60:0:.\t0/1:1/1:3:0,0,3,0:0,0,0,3:36:52:36:32:60:60:2:16\r\n",
      "chr1\t964906\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:2,0,0,0:33:63:0:33:60:60:0:.\t0/1:1/1:4:1,0,3,0:1,0,3,0:28:63:36:37:46:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c9ff5453-4017-40be-88ab-f1e2a5058537/c9ff5453-4017-40be-88ab-f1e2a5058537.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job472770305_index_GQdVBI/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1180954\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:3,2,0,0:0,0,5,0:42:40:0:24:56:56:0:.\t0/1:1/1:2:0,0,1,1:0,2,0,0:33:40:33:33:55:55:2:25\r\n",
      "chr1\t1180957\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:3,2,0,0:0,5,0,0:42:33:0:24:56:56:0:.\t0/1:1/1:4:1,1,1,1:0,2,0,2:5:33:31:32:51:55:2:24\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2cc47f4a-bffd-4ef9-b025-a03cb79eb4e1/2cc47f4a-bffd-4ef9-b025-a03cb79eb4e1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a648b9c4-55bf-4e3d-8de0-38b7b3354a31/a648b9c4-55bf-4e3d-8de0-38b7b3354a31.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2681a0ff-b4f9-4bfb-b0b0-e4a23a990850/2681a0ff-b4f9-4bfb-b0b0-e4a23a990850.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job61175832_index_x9p_i6/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1246652\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:40:0:29:60:60:0:.\t0/1:1/1:2:0,0,1,1:0,0,0,2:33:40:33:33:60:60:2:16\r\n",
      "chr1\t1455542\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:33:9,21,1,2:3,0,30,0:57:22:0:29:46:47:0:.\t0/1:0/1:32:6,20,3,3:6,0,26,0:15:22:15:30,31:43:26,47:2:22\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/ae40d22d-87c6-449f-a065-68a5cb26fc44/ae40d22d-87c6-449f-a065-68a5cb26fc44.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/96a9bc29-ad05-4493-bcf4-6d70975dddc3/96a9bc29-ad05-4493-bcf4-6d70975dddc3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bfcc2678-16d7-4e67-9130-057b0476bdb1/bfcc2678-16d7-4e67-9130-057b0476bdb1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/eb09f0f1-a1d8-411d-bb77-eecd038599ef/eb09f0f1-a1d8-411d-bb77-eecd038599ef.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/94e645ae-366e-4aca-a5db-e80800a33707/94e645ae-366e-4aca-a5db-e80800a33707.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/693cc9a1-20fb-469c-b57b-c5d2862e8886/693cc9a1-20fb-469c-b57b-c5d2862e8886.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/1588b2ec-2863-4ccb-aeda-b73b9195de76/1588b2ec-2863-4ccb-aeda-b73b9195de76.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/86ae836a-eed6-4fa1-9dd2-00ed4b5e9ca1/86ae836a-eed6-4fa1-9dd2-00ed4b5e9ca1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job516018207_index_lSy2cx/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1024082\t.\tT\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:1,4,0,0:0,0,0,5:42:27:0:32:60:60:0:.\t0/1:1/1:3:1,0,1,1:2,0,0,1:4:27:24:28:60:60:2:23\r\n",
      "chr1\t1427406\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:1,2,0,0:0,0,0,3:36:60:0:28:60:60:0:.\t0/1:1/1:4:0,1,2,1:0,3,0,1:28:60:36:33:53:50:2:19\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3f6b8dc3-74af-4677-9c46-59f424f8b8b4/3f6b8dc3-74af-4677-9c46-59f424f8b8b4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job171552488_index_7EW6fQ/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t966426\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:5,0,0,0:0,0,5,0:42:34:0:34:60:60:0:.\t0/1:0/1:4:2,0,2,0:0,2,2,0:25:34:27:35,34:60:60,60:2:24\r\n",
      "chr1\t999842\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:8:1,7,0,0:0,8,0,0:51:27:0:34:60:60:0:.\t0/1:0/1:11:0,8,0,3:3,8,0,0:20:27:20:30,29:60:60,60:2:26\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/59eeffbd-8211-420c-a3bd-baced95416a6/59eeffbd-8211-420c-a3bd-baced95416a6.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/291a955e-cfe4-4d12-bb40-c21fc2834371/291a955e-cfe4-4d12-bb40-c21fc2834371.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f6e5c3e0-99bf-4c2f-954e-850c32d9e910/f6e5c3e0-99bf-4c2f-954e-850c32d9e910.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160310\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job500263790_index_TyhtB_/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t15820\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:34:12,17,5,0:0,0,29,5:49:83:0:33:32:35:0:.\t0/1:0/1:32:11,10,11,0:0,0,21,11:76:83:76:33,33:35:36,34:2:32\r\n",
      "chr1\t187744\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:0,3,0,0:3,0,0,0:36:17:0:23:23:23:0:.\t0/1:1/1:2:0,0,0,2:0,0,2,0:33:17:33:33:23:23:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b92607dc-525a-4695-a47c-071cd37de5f7/b92607dc-525a-4695-a47c-071cd37de5f7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/8dc2f88f-90e0-4790-b1dc-7b10eeca4104/8dc2f88f-90e0-4790-b1dc-7b10eeca4104.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3b559cb3-81f9-4155-af8a-2dd7013d5ed8/3b559cb3-81f9-4155-af8a-2dd7013d5ed8.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job78751889_index_8uMMaK/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t187497\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:95:55,25,12,3:15,0,80,0:60:83:0:28:27:27:0:.\t0/1:0/1:87:44,22,12,9:21,0,66,0:76:83:76:31,29:28:28,29:2:43\r\n",
      "chr1\t971027\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:13:8,5,0,0:0,13,0,0:66:25:0:31:60:60:0:.\t0/1:0/1:7:2,3,1,1:0,5,0,2:18:25:18:18,33:60:60,60:2:25\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/90a63527-ec26-454c-81b7-ac68007ad0eb/90a63527-ec26-454c-81b7-ac68007ad0eb.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job999149087_index_0cGU9j/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t939519\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:0,13,0,1:0,13,1,0:38:19:0:33:60:60:0:.\t0/1:0/1:9:0,7,1,1:2,7,0,0:12:19:12:33,32:61:60,61:2:19\r\n",
      "chr1\t1263119\t.\tT\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:17:13,0,4,0:0,1,3,13:56:16:0:23:60:60:0:.\t0/1:1/1:8:1,0,7,0:0,0,7,1:21:16:30:10:55:55:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d5f9c363-f568-406c-8ee6-2ed3f4bf796d/d5f9c363-f568-406c-8ee6-2ed3f4bf796d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160306\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job584977028_index_O73ikl/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t874301\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:133:58,58,9,8:17,0,116,0:115:62:0:28:51:55:0:.\t0/1:0/1:70:24,27,10,9:19,0,51,0:55:62:55:34,30:44:18,54:2:62\r\n",
      "chr1\t874307\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:132:54,61,9,8:0,17,115,0:124:64:0:32:52:57:0:.\t0/1:0/1:67:27,21,10,9:0,19,48,0:57:64:57:31,33:46:18,57:2:64\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5a10ae7c-0e93-4159-9628-be3da9b766c3/5a10ae7c-0e93-4159-9628-be3da9b766c3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f896d719-8fb7-41fa-98e3-dbf7a7f4532a/f896d719-8fb7-41fa-98e3-dbf7a7f4532a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2905fd44-babc-455c-a8d3-5da61b96e6b0/2905fd44-babc-455c-a8d3-5da61b96e6b0.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160304\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job443410469_index_hVa5YW/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t931147\t.\tA\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:16:0,14,1,1:14,1,0,1:43:20:0:29:60:60:0:.\t0/1:0/1:14:0,10,1,3:10,1,0,3:13:20:13:26,31:60:60,60:2:19\r\n",
      "chr1\t942637\t.\tC\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,2,0,0:33:31:0:32:60:60:0:.\t0/1:1/1:2:0,0,1,1:2,0,0,0:33:31:33:28:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/41783482-0067-4f23-b7f1-24b38d2e7bf1/41783482-0067-4f23-b7f1-24b38d2e7bf1.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/792602af-825a-4b2a-a684-eb9573ba962a/792602af-825a-4b2a-a684-eb9573ba962a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/2d48c751-1a4c-41a3-9cdb-6afdb3f3e5c7/2d48c751-1a4c-41a3-9cdb-6afdb3f3e5c7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e6ccb762-b6f8-4e34-86f6-8bed7cf03a5a/e6ccb762-b6f8-4e34-86f6-8bed7cf03a5a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job330226514_index_EzhFUg/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:10,4,0,0:0,14,0,0:69:21:0:33:20:20:0:.\t0/1:0/1:16:8,5,1,2:0,13,3,0:14:21:14:33,34:24:22,37:2:21\r\n",
      "chr1\t1637362\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:6:5,0,1,0:0,5,1,0:30:31:0:29:55:54:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:24:31:24:33,33:56:53,60:2:24\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/90d23218-8c42-4d47-a779-545b624810c3/90d23218-8c42-4d47-a779-545b624810c3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/0f238983-ce97-42eb-9fb1-bc2dc27cdda3/0f238983-ce97-42eb-9fb1-bc2dc27cdda3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job12756511_index_6L6Ruh/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t185428\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:3:1,2,0,0:3,0,0,0:36:18:0:31:29:29:0:.\t0/1:1/1:2:0,0,0,2:0,0,2,0:33:18:33:31:23:23:2:15\r\n",
      "chr1\t908746\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:2,2,0,0:4,0,0,0:39:21:0:24:47:47:0:.\t0/1:1/1:3:1,0,1,1:1,0,2,0:5:21:19:33:42:33:2:18\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/cd533315-a49b-4d5d-ac36-748d09aa2a88/cd533315-a49b-4d5d-ac36-748d09aa2a88.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job688015949_index_UmYlvb/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t765221\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,4,0,0:39:37:0:34:15:15:0:.\t0/1:0/1:8:0,4,0,4:0,4,0,4:30:37:30:34,29:27:28,25:2:22\r\n",
      "chr1\t1050937\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:8:4,4,0,0:0,0,0,8:51:35:0:32:55:55:0:.\t0/1:1/1:2:0,0,1,1:0,2,0,0:33:35:33:30:60:60:2:31\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/194e6508-7d99-4cfb-8bf5-f036473aa76c/194e6508-7d99-4cfb-8bf5-f036473aa76c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d0cc82cf-52c6-4b72-864a-2691cb7878a2/d0cc82cf-52c6-4b72-864a-2691cb7878a2.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/5c598334-1e51-4793-b029-cc5903e185ae/5c598334-1e51-4793-b029-cc5903e185ae.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a14f5ad5-ff5d-4d96-abc7-d4a55cd683b7/a14f5ad5-ff5d-4d96-abc7-d4a55cd683b7.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/3b66f4aa-ffe6-448d-8948-ff0322fe6bda/3b66f4aa-ffe6-448d-8948-ff0322fe6bda.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/f534ac38-208b-4386-87c6-df99e3dcbd73/f534ac38-208b-4386-87c6-df99e3dcbd73.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/74c2a655-15e8-4cb7-b6fe-d07decf92c70/74c2a655-15e8-4cb7-b6fe-d07decf92c70.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/71aed459-18b1-4d07-b00b-7852f5937f0a/71aed459-18b1-4d07-b00b-7852f5937f0a.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160305\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job729510122_index_v9ifsR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1050070\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:8:4,4,0,0:0,0,8,0:51:29:0:16:32:32:0:.\t0/1:0/1:18:9,5,4,0:4,0,14,0:22:29:22:31,11:33:60,26:2:28\r\n",
      "chr1\t1071904\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:1,1,0,0:0,0,2,0:33:40:0:30:60:60:0:.\t0/1:1/1:2:0,0,1,1:0,0,0,2:33:40:33:33:60:60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/18fdd607-4b46-4dd5-863e-ff40a80e4b0c/18fdd607-4b46-4dd5-863e-ff40a80e4b0c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job461517664_index_v4A5eX/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t187497\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:61:38,18,5,0:5,0,56,0:114:53:0:28:26:27:0:.\t0/1:0/1:66:38,14,9,5:14,0,52,0:46:53:46:33,29:26:26,25:2:53\r\n",
      "chr1\t1183055\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:11:1,10,0,0:0,0,11,0:60:15:0:31:60:60:0:.\t0/1:0/1:17:3,11,1,2:0,0,14,3:8:15:8:32,30:60:60,60:2:15\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d689b050-7d3a-48bb-8e6a-125239c364db/d689b050-7d3a-48bb-8e6a-125239c364db.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job630016258_index_dYVOxS/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t602209\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:33:25:0:34:19:19:0:.\t0/1:1/1:2:0,0,0,2:0,2,0,0:33:25:33:30:28:28:2:15\r\n",
      "chr1\t863797\t.\tG\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,2,0:33:33:0:31:60:60:0:.\t0/1:0/1:4:2,0,2,0:0,2,2,0:23:33:26:35,33:54:48,60:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/83143db6-9bb4-420a-a7c5-2abce396da2e/83143db6-9bb4-420a-a7c5-2abce396da2e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b2cb90b0-6ff5-42b7-96c2-f10df30f470d/b2cb90b0-6ff5-42b7-96c2-f10df30f470d.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160316\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job705649442_index_AA_Iov/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t964383\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:2,2,0,0:0,0,4,0:39:33:0:32:60:60:0:.\t0/1:0/1:4:1,1,1,1:0,0,2,2:21:33:26:30,32:60:60,60:2:22\r\n",
      "chr1\t1048976\t.\tT\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:5,9,0,0:0,0,0,14:69:21:0:28:60:60:0:.\t0/1:0/1:8:4,2,1,1:2,0,0,6:14:21:14:32,31:60:60,60:2:21\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/535f03d3-a012-4ff5-a75d-96e31445a6b4/535f03d3-a012-4ff5-a75d-96e31445a6b4.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!cat head.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "metadata": {},
   "outputs": [],
   "source": [
    "tmpStr=str(file_content)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ordinary string\n"
     ]
    }
   ],
   "source": [
    "def whatisthis(s):\n",
    "    if isinstance(s, str):\n",
    "        print (\"ordinary string\")\n",
    "    elif isinstance(s, unicode):\n",
    "        print (\"unicode string\")\n",
    "    else:\n",
    "        print (\"not a string\")\n",
    "whatisthis(file_content)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 113,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'fileformat' in file_content"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 123,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'##fileform'"
      ]
     },
     "execution_count": 123,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "file_content[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "##fileformat=VCFv4.1\r\n",
      "##FILTER=<ID=PASS,Description=\"Accept as a confident somatic mutation\">\r\n",
      "##FILTER=<ID=Tier1,Description=\"Confident level 1\">\r\n",
      "##FILTER=<ID=Tier2,Description=\"Confident level 2\">\r\n",
      "##FILTER=<ID=Tier3,Description=\"Confident level 3\">\r\n",
      "##FILTER=<ID=Tier4,Description=\"Confident level 4\">\r\n",
      "##FILTER=<ID=Tier5,Description=\"Confident level 5\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read depth at this position in the sample\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Depth of reads supporting alleles 0/1/2/3...\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality for reads supporting alleles\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##TUMOR=\"Sample=TCGA-DU-5874-01A-11D-1705-08,File=/var/lib/cwl/job178108365_input_5fUL1E/C494.TCGA-DU-5874-01A-11D-1705-08.5_gdc_realn.bam\"\r\n",
      "##NORMAL=\"Sample=TCGA-DU-5874-10A-01D-1705-08,File=/var/lib/cwl/job178108365_input_5fUL1E/C494.TCGA-DU-5874-10A-01D-1705-08.5_gdc_realn.bam\"\r\n",
      "##MuSE_version=\"v1.0rc Build Date Aug  6 2015 Build Time 10:11:56\"\r\n",
      "##MuSE_call_1=\"call -f /var/lib/cwl/job178108365_index_0nC40p/GRCh38.d1.vd1.fa -r chr7:1-50000000 -O /var/spool/cwl/call/output.0 /var/lib/cwl/job178108365_input_5fUL1E/C494.TCGA-DU-5874-01A-11D-1705-08.5_gdc_realn.bam /var/lib/cwl/job178108365_input_5fUL1E/C494.TCGA-DU-5874-10A-01D-1705-08.5_gdc_realn.bam\"\r\n",
      "##MuSE_sump=\"sump -I /var/lib/cwl/job408821879_workdir_99LxilPea478/C494.TCGA-DU-5874-01A-11D-1705-08.5_gdc_realn.MuSE.txt -E -O 09d7a024-9dee-4d4c-8591-be09cdbdfb77.vcf -D /var/lib/cwl/job408821879_index_0nC40p/dbsnp_144.grch38.vcf.bgz\"\r\n",
      "##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>\r\n",
      "##contig=<ID=chr2,length=242193529,assembly=GRCh38.d1.vd1>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##FILTER=<ID=PASS,Description=\"Accept as a confident somatic mutation\">\r\n",
      "##FILTER=<ID=Tier1,Description=\"Confident level 1\">\r\n",
      "##FILTER=<ID=Tier2,Description=\"Confident level 2\">\r\n",
      "##FILTER=<ID=Tier3,Description=\"Confident level 3\">\r\n",
      "##FILTER=<ID=Tier4,Description=\"Confident level 4\">\r\n",
      "##FILTER=<ID=Tier5,Description=\"Confident level 5\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read depth at this position in the sample\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Depth of reads supporting alleles 0/1/2/3...\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality for reads supporting alleles\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##TUMOR=\"Sample=TCGA-TQ-A7RG-01A-11D-A33T-08,File=/var/lib/cwl/job214646024_input_3HzcpP/C494.TCGA-TQ-A7RG-01A-11D-A33T-08.1_gdc_realn.bam\"\r\n",
      "##NORMAL=\"Sample=TCGA-TQ-A7RG-10A-01D-A33W-08,File=/var/lib/cwl/job214646024_input_3HzcpP/C494.TCGA-TQ-A7RG-10A-01D-A33W-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_version=\"v1.0rc Build Date Aug  6 2015 Build Time 10:11:56\"\r\n",
      "##MuSE_call_1=\"call -f /var/lib/cwl/job214646024_index_TqPhA6/GRCh38.d1.vd1.fa -r chr18:1-50000000 -O /var/spool/cwl/call/output.0 /var/lib/cwl/job214646024_input_3HzcpP/C494.TCGA-TQ-A7RG-01A-11D-A33T-08.1_gdc_realn.bam /var/lib/cwl/job214646024_input_3HzcpP/C494.TCGA-TQ-A7RG-10A-01D-A33W-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_sump=\"sump -I /var/lib/cwl/job273135982_workdir_ndECT1HncOCk/C494.TCGA-TQ-A7RG-01A-11D-A33T-08.1_gdc_realn.MuSE.txt -E -O 6ecc68de-4217-419c-ad61-591e314e655e.vcf -D /var/lib/cwl/job273135982_index_TqPhA6/dbsnp_144.grch38.vcf.bgz\"\r\n",
      "##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>\r\n",
      "##contig=<ID=chr2,length=242193529,assembly=GRCh38.d1.vd1>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##FILTER=<ID=PASS,Description=\"Accept as a confident somatic mutation\">\r\n",
      "##FILTER=<ID=Tier1,Description=\"Confident level 1\">\r\n",
      "##FILTER=<ID=Tier2,Description=\"Confident level 2\">\r\n",
      "##FILTER=<ID=Tier3,Description=\"Confident level 3\">\r\n",
      "##FILTER=<ID=Tier4,Description=\"Confident level 4\">\r\n",
      "##FILTER=<ID=Tier5,Description=\"Confident level 5\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read depth at this position in the sample\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Depth of reads supporting alleles 0/1/2/3...\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality for reads supporting alleles\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##TUMOR=\"Sample=TCGA-RY-A845-01A-11D-A36O-08,File=/var/lib/cwl/job472013018_input_fKCH9P/C494.TCGA-RY-A845-01A-11D-A36O-08.1_gdc_realn.bam\"\r\n",
      "##NORMAL=\"Sample=TCGA-RY-A845-10A-01D-A367-08,File=/var/lib/cwl/job472013018_input_fKCH9P/C494.TCGA-RY-A845-10A-01D-A367-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_version=\"v1.0rc Build Date Aug  6 2015 Build Time 10:11:56\"\r\n",
      "##MuSE_call_1=\"call -f /var/lib/cwl/job472013018_reference/GRCh38.d1.vd1.fa -r chr6:1-50000000 -O /var/spool/cwl/call/output.0 /var/lib/cwl/job472013018_input_fKCH9P/C494.TCGA-RY-A845-01A-11D-A36O-08.1_gdc_realn.bam /var/lib/cwl/job472013018_input_fKCH9P/C494.TCGA-RY-A845-10A-01D-A367-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_sump=\"sump -I /var/lib/cwl/job26216091_workdir_ixtr8Sjding6/C494.TCGA-RY-A845-01A-11D-A36O-08.1_gdc_realn.MuSE.txt -E -O 6a640b52-648e-4c47-b8a2-c80c7f813e4c.vcf -D /var/lib/cwl/job26216091_reference/dbsnp_144.grch38.vcf.bgz\"\r\n",
      "##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>\r\n",
      "##contig=<ID=chr2,length=242193529,assembly=GRCh38.d1.vd1>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##FILTER=<ID=PASS,Description=\"Accept as a confident somatic mutation\">\r\n",
      "##FILTER=<ID=Tier1,Description=\"Confident level 1\">\r\n",
      "##FILTER=<ID=Tier2,Description=\"Confident level 2\">\r\n",
      "##FILTER=<ID=Tier3,Description=\"Confident level 3\">\r\n",
      "##FILTER=<ID=Tier4,Description=\"Confident level 4\">\r\n",
      "##FILTER=<ID=Tier5,Description=\"Confident level 5\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read depth at this position in the sample\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Depth of reads supporting alleles 0/1/2/3...\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality for reads supporting alleles\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##TUMOR=\"Sample=TCGA-HW-8321-01A-11D-2395-08,File=/var/lib/cwl/job413866067_input_vYlv1y/C494.TCGA-HW-8321-01A-11D-2395-08.1_gdc_realn.bam\"\r\n",
      "##NORMAL=\"Sample=TCGA-HW-8321-10A-01D-2396-08,File=/var/lib/cwl/job413866067_input_vYlv1y/C494.TCGA-HW-8321-10A-01D-2396-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_version=\"v1.0rc Build Date Aug  6 2015 Build Time 10:11:56\"\r\n",
      "##MuSE_call_1=\"call -f /var/lib/cwl/job413866067_reference/GRCh38.d1.vd1.fa -r chrM:1-16569 -O /var/spool/cwl/call/output.0 /var/lib/cwl/job413866067_input_vYlv1y/C494.TCGA-HW-8321-01A-11D-2395-08.1_gdc_realn.bam /var/lib/cwl/job413866067_input_vYlv1y/C494.TCGA-HW-8321-10A-01D-2396-08.1_gdc_realn.bam\"\r\n",
      "##MuSE_sump=\"sump -I /var/lib/cwl/job909254120_workdir_JNKeb_z15nC8/C494.TCGA-HW-8321-01A-11D-2395-08.1_gdc_realn.MuSE.txt -E -O /var/spool/cwl/57e048ed-5681-413e-bbdc-0ff202566744.vcf -D /var/lib/cwl/job909254120_reference/dbsnp_144.grch38.vcf.bgz\"\r\n",
      "##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>\r\n",
      "##contig=<ID=chr2,length=242193529,assembly=GRCh38.d1.vd1>\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/99690673-b98b-496c-bf5e-e08d3b3dc545/99690673-b98b-496c-bf5e-e08d3b3dc545.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job127557346_index_O09uzk/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1020217\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,2,0:33:36:0:26:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,0,0,2:33:36:33:33:60:60:2:16\r\n",
      "chr1\t1022591\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:9:0,9,0,0:0,0,9,0:54:60:0:33:52:52:0:.\t0/1:0/1:15:0,10,0,5:5,0,10,0:53:60:53:32,33:54:60,52:2:37\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c48297db-2dcd-4216-9033-f9bdbe433775/c48297db-2dcd-4216-9033-f9bdbe433775.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/dbfb00be-ed30-402f-bb2e-19e7d0ec340f/dbfb00be-ed30-402f-bb2e-19e7d0ec340f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4aa94453-1f1c-4120-864e-6b018f10704e/4aa94453-1f1c-4120-864e-6b018f10704e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/52615c7e-1274-4513-bd11-c063aef4ae0f/52615c7e-1274-4513-bd11-c063aef4ae0f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/99690673-b98b-496c-bf5e-e08d3b3dc545/99690673-b98b-496c-bf5e-e08d3b3dc545.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160307\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job127557346_index_O09uzk/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t1020217\t.\tG\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,2,0:33:36:0:26:60:60:0:.\t0/1:1/1:2:0,0,2,0:0,0,0,2:33:36:33:33:60:60:2:16\r\n",
      "chr1\t1022591\t.\tG\tA\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:9:0,9,0,0:0,0,9,0:54:60:0:33:52:52:0:.\t0/1:0/1:15:0,10,0,5:5,0,10,0:53:60:53:32,33:54:60,52:2:37\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c48297db-2dcd-4216-9033-f9bdbe433775/c48297db-2dcd-4216-9033-f9bdbe433775.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/dbfb00be-ed30-402f-bb2e-19e7d0ec340f/dbfb00be-ed30-402f-bb2e-19e7d0ec340f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/4aa94453-1f1c-4120-864e-6b018f10704e/4aa94453-1f1c-4120-864e-6b018f10704e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/52615c7e-1274-4513-bd11-c063aef4ae0f/52615c7e-1274-4513-bd11-c063aef4ae0f.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/eef4b992-9147-45d9-9530-eaf2fedb2015/eef4b992-9147-45d9-9530-eaf2fedb2015.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/b8d00849-003c-4675-b1ca-1382316a0c93/b8d00849-003c-4675-b1ca-1382316a0c93.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job752047669_index_yaoK3P/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t183800\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:14:6,7,1,0:0,13,1,0:47:33:0:33:22:22:0:.\t0/1:0/1:21:12,4,3,2:0,16,5,0:26:33:26:29,34:27:27,25:2:28\r\n",
      "chr1\t1290155\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,0,0,2:28:26:0:26:23:23:0:.\t0/1:1/1:5:3,0,2,0:0,2,0,3:10:26:29:33:31:47:2:16\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d061c5fb-87d1-451e-a257-eaee4e7af7a9/d061c5fb-87d1-451e-a257-eaee4e7af7a9.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/c6c7dae7-60be-4acc-b6c8-2866858d0194/c6c7dae7-60be-4acc-b6c8-2866858d0194.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/6f824911-c2d5-4c4b-b1a1-377fe4b8844e/6f824911-c2d5-4c4b-b1a1-377fe4b8844e.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/d6084f6a-122c-4efb-a2bf-ef50024373f3/d6084f6a-122c-4efb-a2bf-ef50024373f3.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160309\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job170879263_index_UUzyAz/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t933015\t.\tC\tT\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:2:2,0,0,0:0,2,0,0:33:23:0:32:60:60:0:.\t0/1:0/1:5:3,0,1,1:0,3,0,2:16:23:16:32,29:60:60,60:2:15\r\n",
      "chr1\t948731\t.\tT\tC\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:4:0,4,0,0:0,0,0,4:39:24:0:31:60:60:0:.\t0/1:0/1:10:0,7,0,3:0,3,0,7:17:24:17:28,29:60:60,60:2:20\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/51946e4b-3a0b-40d5-84b0-9c08f44c7098/51946e4b-3a0b-40d5-84b0-9c08f44c7098.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3b48fa3-a040-450f-9d33-efdac2537717/a3b48fa3-a040-450f-9d33-efdac2537717.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.1\r\n",
      "##fileDate=20160317\r\n",
      "##phasing=none\r\n",
      "##reference=file:///var/lib/cwl/job569970468_index_b3SOZR/GRCh38.d1.vd1.fa\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=IGT,Number=1,Type=String,Description=\"Genotype when called independently (only filled if called in joint prior mode)\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\r\n",
      "##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description=\"Occurrence count for each base at this site (A,C,G,T)\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">\r\n",
      "##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description=\"Joint genotype quality (only filled if called in join prior mode)\">\r\n",
      "##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description=\"Variant allele quality\">\r\n",
      "##FORMAT=<ID=BQ,Number=.,Type=Integer,Description=\"Average base quality\">\r\n",
      "##FORMAT=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality across all reads\">\r\n",
      "##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description=\"Average mapping quality for each allele present in the genotype\">\r\n",
      "##FORMAT=<ID=SS,Number=1,Type=Integer,Description=\"Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown\">\r\n",
      "##FORMAT=<ID=SSC,Number=1,Type=Integer,Description=\"Somatic Score\">\r\n",
      "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\r\n",
      "chr1\t14574\t.\tA\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:15:13,0,2,0:13,0,2,0:47:19:0:33:21:23:0:.\t0/1:0/1:15:9,1,5,0:10,0,5,0:12:19:12:33,27:24:24,22:2:19\r\n",
      "chr1\t1312209\t.\tC\tG\t.\t.\t.\tGT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC\t0/0:0/0:5:0,5,0,0:0,5,0,0:42:18:0:10:39:39:0:.\t0/1:0/1:8:2,2,2,2:0,4,4,0:11:18:11:16,15:46:32,60:2:17\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd/e07cb0ce-48a1-42b7-9c21-63d2de64b8cd.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/44663ff0-2002-4e7d-a6ca-8c834f8698da/44663ff0-2002-4e7d-a6ca-8c834f8698da.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/bcd38101-c9e3-4d7e-8951-3a0434474187/bcd38101-c9e3-4d7e-8951-3a0434474187.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n",
      "/nrnb/users/btsui/Data/tcga_orig_vcf/a3650193-4824-4db6-bbb8-7471324b2d7b/a3650193-4824-4db6-bbb8-7471324b2d7b.vcf.gz\r\n",
      "\r\n",
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=alt_allele_in_normal,Description=\"Evidence seen in the normal sample\">\r\n",
      "##FILTER=<ID=clustered_events,Description=\"Clustered events observed in the tumor\">\r\n",
      "##FILTER=<ID=germline_risk,Description=\"Evidence indicates this site is germline, not somatic\">\r\n",
      "##FILTER=<ID=homologous_mapping_event,Description=\"More than three events were observed in the tumor\">\r\n",
      "##FILTER=<ID=multi_event_alt_allele_in_normal,Description=\"Multiple events observed in tumor and normal\">\r\n",
      "##FILTER=<ID=panel_of_normals,Description=\"Seen in at least 2 samples in the panel of normals\">\r\n",
      "##FILTER=<ID=str_contraction,Description=\"Site filtered due to contraction of short tandem repeat region\">\r\n",
      "##FILTER=<ID=t_lod_fstar,Description=\"Tumor does not meet likelihood threshold\">\r\n",
      "##FILTER=<ID=triallelic_site,Description=\"Site filtered because more than two alt alleles pass tumor LOD\">\r\n",
      "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=AF,Number=1,Type=Float,Description=\"Allele fraction of the event in the tumor\">\r\n",
      "##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description=\"Count of reads in F1R2 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description=\"Count of reads in F2R1 pair orientation supporting the alternate allele\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
      "##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description=\"Fraction of alt reads indicating OxoG error\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=PGT,Number=1,Type=String,Description=\"Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another\">\r\n",
      "##FORMAT=<ID=PID,Number=1,Type=String,Description=\"Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group\">\r\n",
      "\r\n",
      "\r\n"
     ]
    }
   ],
   "source": [
    "!cat head.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "176 head.txt\r\n"
     ]
    }
   ],
   "source": [
    "!wc -l head.txt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "##fileformat=VCFv4.2\r\n",
      "##FILTER=<ID=indelError,Description=\"Likely artifact due to indel reads at this position\">\r\n",
      "##FILTER=<ID=str10,Description=\"Less than 10% or more than 90% of variant supporting reads on one strand\">\r\n",
      "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
      "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\r\n",
      "##FORMAT=<ID=DP4,Number=1,Type=String,Description=\"Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev\">\r\n",
      "##FORMAT=<ID=FREQ,Number=1,Type=String,Description=\"Variant allele frequency\">\r\n",
      "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
      "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
      "##FORMAT=<ID=RD,Number=1,Type=Integer,Description=\"Depth of reference-supporting bases (reads1)\">\r\n",
      "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total depth of quality bases\">\r\n",
      "##INFO=<ID=GPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls\">\r\n",
      "##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=\"Indicates if record is a somatic mutation\">\r\n",
      "##INFO=<ID=SPV,Number=1,Type=Float,Description=\"Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls\">\r\n",
      "##INFO=<ID=SS,Number=1,Type=String,Description=\"Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)\">\r\n",
      "##INFO=<ID=SSC,Number=1,Type=String,Description=\"Somatic score in Phred scale (0-255) derived from somatic p-value\">\r\n",
      "##contig=<ID=chr1,length=248956422>\r\n",
      "##contig=<ID=chr2,length=242193529>\r\n",
      "##contig=<ID=chr3,length=198295559>\r\n",
      "##contig=<ID=chr4,length=190214555>\r\n",
      "##contig=<ID=chr5,length=181538259>\r\n",
      "##contig=<ID=chr6,length=170805979>\r\n",
      "##contig=<ID=chr7,length=159345973>\r\n",
      "##contig=<ID=chr8,length=145138636>\r\n",
      "##contig=<ID=chr9,length=138394717>\r\n",
      "##contig=<ID=chr10,length=133797422>\r\n",
      "##contig=<ID=chr11,length=135086622>\r\n",
      "##contig=<ID=chr12,length=133275309>\r\n",
      "##contig=<ID=chr13,length=114364328>\r\n",
      "##contig=<ID=chr14,length=107043718>\r\n",
      "##contig=<ID=chr15,length=101991189>\r\n",
      "##contig=<ID=chr16,length=90338345>\r\n",
      "##contig=<ID=chr17,length=83257441>\r\n",
      "##contig=<ID=chr18,length=80373285>\r\n",
      "##contig=<ID=chr19,length=58617616>\r\n",
      "##contig=<ID=chr20,length=64444167>\r\n",
      "##contig=<ID=chr21,length=46709983>\r\n",
      "##contig=<ID=chr22,length=50818468>\r\n",
      "##contig=<ID=chrX,length=156040895>\r\n",
      "##contig=<ID=chrY,length=57227415>\r\n",
      "##contig=<ID=chrM,length=16569>\r\n",
      "##contig=<ID=chr1_KI270706v1_random,length=175055>\r\n",
      "##contig=<ID=chr1_KI270707v1_random,length=32032>\r\n",
      "##contig=<ID=chr1_KI270708v1_random,length=127682>\r\n",
      "##contig=<ID=chr1_KI270709v1_random,length=66860>\r\n",
      "##contig=<ID=chr1_KI270710v1_random,length=40176>\r\n",
      "##contig=<ID=chr1_KI270711v1_random,length=42210>\r\n",
      "##contig=<ID=chr1_KI270712v1_random,length=176043>\r\n",
      "##contig=<ID=chr1_KI270713v1_random,length=40745>\r\n",
      "##contig=<ID=chr1_KI270714v1_random,length=41717>\r\n",
      "##contig=<ID=chr2_KI270715v1_random,length=161471>\r\n",
      "##contig=<ID=chr2_KI270716v1_random,length=153799>\r\n",
      "##contig=<ID=chr3_GL000221v1_random,length=155397>\r\n",
      "##contig=<ID=chr4_GL000008v2_random,length=209709>\r\n",
      "##contig=<ID=chr5_GL000208v1_random,length=92689>\r\n",
      "##contig=<ID=chr9_KI270717v1_random,length=40062>\r\n",
      "##contig=<ID=chr9_KI270718v1_random,length=38054>\r\n",
      "##contig=<ID=chr9_KI270719v1_random,length=176845>\r\n",
      "##contig=<ID=chr9_KI270720v1_random,length=39050>\r\n",
      "##contig=<ID=chr11_KI270721v1_random,length=100316>\r\n",
      "##contig=<ID=chr14_GL000009v2_random,length=201709>\r\n",
      "##contig=<ID=chr14_GL000225v1_random,length=211173>\r\n",
      "##contig=<ID=chr14_KI270722v1_random,length=194050>\r\n",
      "##contig=<ID=chr14_GL000194v1_random,length=191469>\r\n",
      "##contig=<ID=chr14_KI270723v1_random,length=38115>\r\n",
      "##contig=<ID=chr14_KI270724v1_random,length=39555>\r\n",
      "##contig=<ID=chr14_KI270725v1_random,length=172810>\r\n",
      "##contig=<ID=chr14_KI270726v1_random,length=43739>\r\n",
      "##contig=<ID=chr15_KI270727v1_random,length=448248>\r\n",
      "##contig=<ID=chr16_KI270728v1_random,length=1872759>\r\n",
      "##contig=<ID=chr17_GL000205v2_random,length=185591>\r\n",
      "##contig=<ID=chr17_KI270729v1_random,length=280839>\r\n",
      "##contig=<ID=chr17_KI270730v1_random,length=112551>\r\n",
      "##contig=<ID=chr22_KI270731v1_random,length=150754>\r\n",
      "##contig=<ID=chr22_KI270732v1_random,length=41543>\r\n",
      "##contig=<ID=chr22_KI270733v1_random,length=179772>\r\n",
      "##contig=<ID=chr22_KI270734v1_random,length=165050>\r\n",
      "##contig=<ID=chr22_KI270735v1_random,length=42811>\r\n",
      "##contig=<ID=chr22_KI270736v1_random,length=181920>\r\n",
      "##contig=<ID=chr22_KI270737v1_random,length=103838>\r\n",
      "##contig=<ID=chr22_KI270738v1_random,length=99375>\r\n",
      "##contig=<ID=chr22_KI270739v1_random,length=73985>\r\n",
      "##contig=<ID=chrY_KI270740v1_random,length=37240>\r\n",
      "##contig=<ID=chrUn_KI270302v1,length=2274>\r\n",
      "##contig=<ID=chrUn_KI270304v1,length=2165>\r\n",
      "##contig=<ID=chrUn_KI270303v1,length=1942>\r\n",
      "##contig=<ID=chrUn_KI270305v1,length=1472>\r\n",
      "##contig=<ID=chrUn_KI270322v1,length=21476>\r\n",
      "##contig=<ID=chrUn_KI270320v1,length=4416>\r\n",
      "##contig=<ID=chrUn_KI270310v1,length=1201>\r\n",
      "##contig=<ID=chrUn_KI270316v1,length=1444>\r\n",
      "##contig=<ID=chrUn_KI270315v1,length=2276>\r\n",
      "##contig=<ID=chrUn_KI270312v1,length=998>\r\n",
      "##contig=<ID=chrUn_KI270311v1,length=12399>\r\n",
      "##contig=<ID=chrUn_KI270317v1,length=37690>\r\n",
      "##contig=<ID=chrUn_KI270412v1,length=1179>\r\n",
      "##contig=<ID=chrUn_KI270411v1,length=2646>\r\n",
      "##contig=<ID=chrUn_KI270414v1,length=2489>\r\n",
      "##contig=<ID=chrUn_KI270419v1,length=1029>\r\n",
      "##contig=<ID=chrUn_KI270418v1,length=2145>\r\n",
      "\r\n",
      "gzip: stdout: Broken pipe\r\n"
     ]
    }
   ],
   "source": [
    "!gunzip -c  /nrnb/users/btsui/Data/tcga_orig_vcf/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c/bcc7d112-2d5d-4ff1-a863-70f11d5b0f2c.vcf.gz | head -n 100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 152,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"data\": {\n",
      "    \"data_type\": \"Raw Simple Somatic Mutation\",\n",
      "    \"updated_datetime\": \"2018-02-15T06:59:15.267328-06:00\",\n",
      "    \"created_datetime\": \"2017-12-01T01:01:39.435980-06:00\",\n",
      "    \"file_name\": \"9ad50bf6-9fe0-4ad7-b26f-b6f52824ef9e.vcf.gz\",\n",
      "    \"md5sum\": \"ff04b9d4d914e2f63a3fd376e6f0354b\",\n",
      "    \"data_format\": \"VCF\",\n",
      "    \"acl\": [\n",
      "      \"phs000178\"\n",
      "    ],\n",
      "    \"access\": \"controlled\",\n",
      "    \"state\": \"live\",\n",
      "    \"file_id\": \"9ad50bf6-9fe0-4ad7-b26f-b6f52824ef9e\",\n",
      "    \"data_category\": \"Simple Nucleotide Variation\",\n",
      "    \"file_size\": 44664,\n",
      "    \"submitter_id\": \"TCGA-TQ-A7RI-01A-11D-A33T-08_TCGA-TQ-A7RI-10A-01D-A33W-08_varscan_dr_10.0\",\n",
      "    \"type\": \"simple_somatic_mutation\",\n",
      "    \"file_state\": \"submitted\",\n",
      "    \"experimental_strategy\": \"WXS\"\n",
      "  },\n",
      "  \"warnings\": {}\n",
      "}\n"
     ]
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Analysis ID\t\n",
    "#submitter_id might do, "
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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