##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
##contig=<ID=chr11,length=135006516,assembly=hg19>
##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
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##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
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##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
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##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
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##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
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##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
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##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE|ALLELE_NUM">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M10475	M10478	M10500	M128215
chr1	10001	.	T	TC	175.91	.	AC=4;AF=0.50;AN=8;BaseQRankSum=4.975;DP=76;FS=12.516;HRun=0;HaplotypeScore=218.6157;MQ=35.31;MQ0=0;MQRankSum=-0.238;QD=2.31;ReadPosRankSum=2.910;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/1:10,2:15:10.41:25,0,10	0/1:10,4:16:5.30:40,0,5	0/1:10,10:21:7.48:111,0,7	0/1:15,5:24:0.26:49,0,0
chr1	10056	.	A	C	47.27	.	AC=1;AF=0.13;AN=8;BaseQRankSum=-1.865;DP=199;Dels=0.00;FS=7.175;HRun=0;HaplotypeScore=10.0031;MQ=30.59;MQ0=0;MQRankSum=-1.940;QD=0.65;ReadPosRankSum=1.402;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/0:35,2:39:47.44:0,47,739	0/1:62,11:73:83.28:83,0,1414	0/0:30,0:31:90.20:0,90,983	0/0:56,0:56:99:0,144,1518
chr1	10121	.	A	C	111.08	.	AC=1;AF=0.13;AN=8;BaseQRankSum=0.234;DP=102;Dels=0.00;FS=16.063;HRun=0;HaplotypeScore=9.1907;MQ=29.08;MQ0=0;MQRankSum=0.521;QD=4.63;ReadPosRankSum=-1.401;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/0:20,0:20:39.04:0,39,379	0/0:42,1:48:99:0,102,1011	0/0:10,0:10:30.05:0,30,305	0/1:15,9:24:99:147,0,228
chr1	10177	.	A	C	163.46	.	AC=3;AF=0.38;AN=8;BaseQRankSum=1.016;DP=57;Dels=0.00;FS=6.680;HRun=2;HaplotypeScore=4.4949;MQ=28.39;MQ0=0;MQRankSum=2.046;QD=3.21;ReadPosRankSum=-2.074;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/1:10,4:14:56.38:56,0,143	0/1:24,6:30:69.02:69,0,329	0/0:6,0:6:14.98:0,15,125	0/1:4,3:7:17.60:81,0,18
chr1	10180	.	T	C	79.53	.	AC=2;AF=0.25;AN=8;BaseQRankSum=-0.295;DP=54;Dels=0.00;FS=1.926;HRun=2;HaplotypeScore=4.7635;MQ=28.08;MQ0=0;MQRankSum=0.710;QD=2.41;ReadPosRankSum=-0.814;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/0:12,2:14:5.30:0,5,215	0/1:17,9:26:99:107,0,218	0/1:6,1:7:12.66:13,0,95	0/0:7,0:7:12.02:0,12,121
chr1	10234	.	C	T	49.10	.	AC=2;AF=0.25;AN=8;BaseQRankSum=-2.564;DP=45;Dels=0.00;FS=5.371;HRun=1;HaplotypeScore=7.4331;MQ=31.63;MQ0=0;MQRankSum=1.310;QD=1.36;ReadPosRankSum=3.118;CSQ=upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000456328|||||processed_transcript|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000541675|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000450305|||||transcribed_unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000515242|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000223972|DDX11L1|ENST00000518655|||||transcribed_unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1	GT:AD:DP:GQ:PL	0/1:6,1:7:18.57:19,0,80	0/1:22,6:29:70.92:71,0,463	0/0:4,0:4:12.03:0,12,137	0/0:3,2:5:6.02:0,6,68
chr16	72057282	.	A	G	1098.89	.	AC=5;AF=0.63;AN=8;BaseQRankSum=-0.026;DP=80;Dels=0.00;FS=7.890;HRun=3;HaplotypeScore=1.9993;MQ=36.24;MQ0=0;MQRankSum=0.529;QD=13.74;ReadPosRankSum=1.005;CSQ=intron_variant|||ENSG00000102967|DHODH|ENST00000219240||||-/395|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000102967|DHODH|ENST00000571392|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000572003|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573843|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573922|||||processed_transcript|1,intron_variant|||ENSG00000102967|DHODH|ENST00000574309||||-/193|protein_coding|1,intron_variant|||ENSG00000102967|DHODH|ENST00000572887||||-/393|protein_coding|1	GT:AD:DP:GQ:PL	1/1:0,18:18:39.05:422,39,0	0/1:8,7:16:99:201,0,173	0/1:5,1:6:19.75:20,0,148	0/1:15,23:40:99:501,0,332
chr16	72057435	.	C	T	572.98	.	AC=1;AF=0.13;AN=8;BaseQRankSum=-2.270;DP=260;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.5319;MQ=36.53;MQ0=0;MQRankSum=0.596;QD=8.07;ReadPosRankSum=0.927;CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000102967|DHODH|ENST00000219240|8/9|probably_damaging(0.956)|deleterious(0)|346/395|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000102967|DHODH|ENST00000571392|3/4||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000572003|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573843|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573922|||||processed_transcript|1,intron_variant|||ENSG00000102967|DHODH|ENST00000574309||||-/193|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000102967|DHODH|ENST00000572887|8/9|probably_damaging(0.946)|deleterious(0)|344/393|protein_coding|1	GT:AD:DP:GQ:PL	0/1:37,33:71:99:609,0,666	0/0:56,0:56:99:0,135,1543	0/0:67,1:68:99:0,120,1460	0/0:65,0:65:99:0,180,1982
chr16	72059269	.	T	C	39.18	.	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.59;CSQ=downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000219240||||-/395|protein_coding|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000571392|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000572003|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573843|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573922|||||processed_transcript|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000574309||||-/193|protein_coding|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000572887||||-/393|protein_coding|1	GT:AD:DP:GQ:PL	./.	./.	1/1:0,2:2:6.02:70,6,0	./.