{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "### Running in Docker container on Ostrich\n", "\n", "#### Started Docker container with the following command:\n", "\n", "```docker run - p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:owl_web -v /Users/sam/gitrepos/LabDocs/jupyter_nbs/sam/:/jupyter_nbs -it 0ba43904567e```\n", "\n", "The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.\n", "\n", "Once the container was started, started Jupyter Notebook with the following command inside the Docker container:\n", "\n", "```jupyter notebook```\n", "\n", "This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.\n", "\n", "The Docker container is running on an image created from this [Dockerfile (Git commit 65ab831)](https://github.com/sr320/LabDocs/blob/65ab8317556e01c8b3ae3ca260119b1eb163ed44/code/dockerfiles/Dockerfile.bio)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Thu Nov 17 22:30:49 UTC 2016\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Check computer specs" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "65e23f54bcc9\n" ] } ], "source": [ "%%bash\n", "hostname" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Architecture: x86_64\n", "CPU op-mode(s): 32-bit, 64-bit\n", "Byte Order: Little Endian\n", "CPU(s): 8\n", "On-line CPU(s) list: 0-7\n", "Thread(s) per core: 1\n", "Core(s) per socket: 8\n", "Socket(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 26\n", "Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz\n", "Stepping: 5\n", "CPU MHz: 2260.998\n", "BogoMIPS: 4521.99\n", "Hypervisor vendor: KVM\n", "Virtualization type: full\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 8192K\n" ] } ], "source": [ "%%bash\n", "lscpu" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### View PyRad output files" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 1908968\n", "-rw-rw-rw- 1 srlab staff 260547113 Aug 16 15:46 oly_gbs_pyrad.alleles\n", "-rw-rw-rw- 1 srlab staff 239419515 Aug 16 15:46 oly_gbs_pyrad.excluded_loci\n", "-rw-rw-rw- 1 srlab staff 126920538 Aug 16 15:46 oly_gbs_pyrad.gphocs\n", "-rw-rw-rw- 1 srlab staff 133378169 Aug 16 15:46 oly_gbs_pyrad.loci\n", "-rw-rw-rw- 1 srlab staff 86991 Aug 16 15:47 oly_gbs_pyrad.migrate\n", "-rw-rw-rw- 1 srlab staff 571222263 Aug 16 15:47 oly_gbs_pyrad.nex\n", "-rw-rw-rw- 1 srlab staff 463115051 Aug 16 15:47 oly_gbs_pyrad.phy\n", "-rw-rw-rw- 1 srlab staff 1266466 Aug 16 15:46 oly_gbs_pyrad.phy.partitions\n", "-rw-rw-rw- 1 srlab staff 26795940 Aug 16 15:46 oly_gbs_pyrad.snps\n", "-rw-rw-rw- 1 srlab staff 11519817 Aug 16 15:46 oly_gbs_pyrad.snps.geno\n", "-rwxrwxrwx 1 srlab staff 13474538 Aug 16 22:20 oly_gbs_pyrad.str\n", "-rw-rw-rw- 1 srlab staff 30531 Aug 16 15:46 oly_gbs_pyrad.treemix.gz\n", "-rw-rw-rw- 1 srlab staff 2417961 Aug 16 15:46 oly_gbs_pyrad.unlinked_snps\n", "-rw-rw-rw- 1 srlab staff 2441102 Aug 16 15:46 oly_gbs_pyrad.usnps.geno\n", "-rw-rw-rw- 1 srlab staff 50527186 Aug 16 15:46 oly_gbs_pyrad.vcf\n", "-rw-rw-rw- 1 srlab staff 0 Aug 16 15:51 oly_gbs_pyrad.vcf.fai\n", "-rw-rw-rw- 1 srlab staff 50527182 Aug 16 16:01 oly_gbs_pyrad_no_spaces.vcf\n", "-rw-rw-rw- 1 srlab staff 1056041 Aug 16 16:24 oly_gbs_pyrad_no_spaces.vcf.idx\n" ] } ], "source": [ "%%bash\n", "ls -l /root/owl_web/Athaliana/20160715_pyrad_outfiles" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Make working directory & move PyRad VCF file to working directory" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /root/data/20161117_oly_gbs_vcf_analysis" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "'/root/owl_web/Athaliana/20160715_pyrad_outfiles/oly_gbs_pyrad.vcf' -> '/root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf'\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m2.747s\n", "user\t0m0.000s\n", "sys\t0m0.410s\n" ] } ], "source": [ "%%bash\n", "time cp -avr /root/owl_web/Athaliana/20160715_pyrad_outfiles/oly_gbs_pyrad.vcf /root/data/20161117_oly_gbs_vcf_analysis/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### View the VCF header info" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "##fileformat=VCFv4.1\n", "##fileDate=20160725\n", "##source=pyRAD.v.3.0.66\n", "##reference=common_allele_at_each_locus\n", "##INFO=\n", "##INFO=\n", "##INFO=\n", "##INFO=\n", "##FORMAT=\n", "##FORMAT=\n", "##FORMAT=\n", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO \tFORMAT\t1HL_10A.assembled\t1HL_11A.assembled\t1HL_12A.assembled\t1HL_13A.assembled\t1HL_14A.assembled\t1HL_15A.assembled\t1HL_16A.assembled\t1HL_17A.assembled\t1HL_19A.assembled\t1HL_1A.assembled\t1HL_20A.assembled\t1HL_21A.assembled\t1HL_22A.assembled\t1HL_23A.assembled\t1HL_24A.assembled\t1HL_25A.assembled\t1HL_26A.assembled\t1HL_27A.assembled\t1HL_28A.assembled\t1HL_29A.assembled\t1HL_2A.assembled\t1HL_31A.assembled\t1HL_33A.assembled\t1HL_34A.assembled\t1HL_35A.assembled\t1HL_3A.assembled\t1HL_4A.assembled\t1HL_5A.assembled\t1HL_6A.assembled\t1HL_7A.assembled\t1HL_8A.assembled\t1HL_9A.assembled\t1NF_10A.assembled\t1NF_11A.assembled\t1NF_12A.assembled\t1NF_13A.assembled\t1NF_14A.assembled\t1NF_15A.assembled\t1NF_16A.assembled\t1NF_17A.assembled\t1NF_18A.assembled\t1NF_19A.assembled\t1NF_1A.assembled\t1NF_20A.assembled\t1NF_21A.assembled\t1NF_22A.assembled\t1NF_23A.assembled\t1NF_24A.assembled\t1NF_25A.assembled\t1NF_26A.assembled\t1NF_27A.assembled\t1NF_28A.assembled\t1NF_29A.assembled\t1NF_2A.assembled\t1NF_30A.assembled\t1NF_31A.assembled\t1NF_32A.assembled\t1NF_33A.assembled\t1NF_4A.assembled\t1NF_5A.assembled\t1NF_6A.assembled\t1NF_7A.assembled\t1NF_8A.assembled\t1NF_9A.assembled\t1SN_10A.assembled\t1SN_11A.assembled\t1SN_12A.assembled\t1SN_13A.assembled\t1SN_14A.assembled\t1SN_15A.assembled\t1SN_16A.assembled\t1SN_17A.assembled\t1SN_18A.assembled\t1SN_19A.assembled\t1SN_1A.assembled\t1SN_20A.assembled\t1SN_21A.assembled\t1SN_22A.assembled\t1SN_23A.assembled\t1SN_24A.assembled\t1SN_25A.assembled\t1SN_26A.assembled\t1SN_27A.assembled\t1SN_28A.assembled\t1SN_29A.assembled\t1SN_2A.assembled\t1SN_30A.assembled\t1SN_31A.assembled\t1SN_32A.assembled\t1SN_3A.assembled\t1SN_4A.assembled\t1SN_5A.assembled\t1SN_6A.assembled\t1SN_7A.assembled\t1SN_8A.assembled\t1SN_9A.assembled\n" ] } ], "source": [ "%%bash\n", "head -12 /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### View the header again and perform line count\n", "\n", "#### This is done to show that the last line of the header (with all of the sample names) is truly a single line" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "12\n" ] } ], "source": [ "%%bash\n", "head -12 /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Create population list files - necessary for subsequent vcftools commands\n", "\n", "#### vcftools requires separate population files that list the sample IDs for each individual within each population. The command below uses a for loop to do the following:\n", "\n", "#### ```$(awk 'NR == 12 {print $0}'``` - This uses ```awk``` to process only the 12th line (```NR == 12```) of the file and prints all the fields (```{print $0}```) on that line.\n", "\n", "#### ```if [[ \"$i\" =~ 1HL.* ]] then echo \"$i\" >> /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop``` - A set of if/elif statements that evaluate each field from the awk command and determines if they match a pattern (```[[ \"$i\" =~ 1HL.* ]]```. If they match that pattern, the value currently stored in ```$i``` is written to the appropriate population file." ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m2.496s\n", "user\t0m0.050s\n", "sys\t0m0.900s\n" ] } ], "source": [ "%%bash\n", "time for i in $(awk 'NR == 12 {print $0}' /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf)\n", "do\n", " if [[ \"$i\" =~ 1HL.* ]]\n", " then echo \"$i\" >> /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", " elif [[ \"$i\" =~ 1NF.* ]]\n", " then echo \"$i\" >> /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", " elif [[ \"$i\" =~ 1SN.* ]]\n", " then echo \"$i\" >> /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", " fi\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Verify population files contents" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A.assembled\n", "1HL_11A.assembled\n", "1HL_12A.assembled\n", "1HL_13A.assembled\n", "1HL_14A.assembled\n", "1HL_15A.assembled\n", "1HL_16A.assembled\n", "1HL_17A.assembled\n", "1HL_19A.assembled\n", "1HL_1A.assembled\n", "1HL_20A.assembled\n", "1HL_21A.assembled\n", "1HL_22A.assembled\n", "1HL_23A.assembled\n", "1HL_24A.assembled\n", "1HL_25A.assembled\n", "1HL_26A.assembled\n", "1HL_27A.assembled\n", "1HL_28A.assembled\n", "1HL_29A.assembled\n", "1HL_2A.assembled\n", "1HL_31A.assembled\n", "1HL_33A.assembled\n", "1HL_34A.assembled\n", "1HL_35A.assembled\n", "1HL_3A.assembled\n", "1HL_4A.assembled\n", "1HL_5A.assembled\n", "1HL_6A.assembled\n", "1HL_7A.assembled\n", "1HL_8A.assembled\n", "1HL_9A.assembled\n" ] } ], "source": [ "%%bash\n", "cat /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1NF_10A.assembled\n", "1NF_11A.assembled\n", "1NF_12A.assembled\n", "1NF_13A.assembled\n", "1NF_14A.assembled\n", "1NF_15A.assembled\n", "1NF_16A.assembled\n", "1NF_17A.assembled\n", "1NF_18A.assembled\n", "1NF_19A.assembled\n", "1NF_1A.assembled\n", "1NF_20A.assembled\n", "1NF_21A.assembled\n", "1NF_22A.assembled\n", "1NF_23A.assembled\n", "1NF_24A.assembled\n", "1NF_25A.assembled\n", "1NF_26A.assembled\n", "1NF_27A.assembled\n", "1NF_28A.assembled\n", "1NF_29A.assembled\n", "1NF_2A.assembled\n", "1NF_30A.assembled\n", "1NF_31A.assembled\n", "1NF_32A.assembled\n", "1NF_33A.assembled\n", "1NF_4A.assembled\n", "1NF_5A.assembled\n", "1NF_6A.assembled\n", "1NF_7A.assembled\n", "1NF_8A.assembled\n", "1NF_9A.assembled\n" ] } ], "source": [ "%%bash\n", "cat /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1SN_10A.assembled\n", "1SN_11A.assembled\n", "1SN_12A.assembled\n", "1SN_13A.assembled\n", "1SN_14A.assembled\n", "1SN_15A.assembled\n", "1SN_16A.assembled\n", "1SN_17A.assembled\n", "1SN_18A.assembled\n", "1SN_19A.assembled\n", "1SN_1A.assembled\n", "1SN_20A.assembled\n", "1SN_21A.assembled\n", "1SN_22A.assembled\n", "1SN_23A.assembled\n", "1SN_24A.assembled\n", "1SN_25A.assembled\n", "1SN_26A.assembled\n", "1SN_27A.assembled\n", "1SN_28A.assembled\n", "1SN_29A.assembled\n", "1SN_2A.assembled\n", "1SN_30A.assembled\n", "1SN_31A.assembled\n", "1SN_32A.assembled\n", "1SN_3A.assembled\n", "1SN_4A.assembled\n", "1SN_5A.assembled\n", "1SN_6A.assembled\n", "1SN_7A.assembled\n", "1SN_8A.assembled\n", "1SN_9A.assembled\n" ] } ], "source": [ "%%bash\n", "cat /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Verify each population file has expected number of individuals (32)" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "32 /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "32 /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "32 /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n" ] } ], "source": [ "%%bash\n", "for i in /root/data/20161117_oly_gbs_vcf_analysis/*.pop\n", "do\n", " wc -l \"$i\"\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Verify instllation of vcftools" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bin/vcftools\n" ] } ], "source": [ "%%bash\n", "which vcftools" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Determine Fst values between all population combinations" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1HL vs. 1NF" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "VCFtools - 0.1.14\n", "(C) Adam Auton and Anthony Marcketta 2009\n", "\n", "Parameters as interpreted:\n", "\t--vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\n", "Eighth Header entry should be INFO: INFO \n", "Keeping individuals in 'keep' list\n", "After filtering, kept 64 out of 96 Individuals\n", "Outputting Weir and Cockerham Fst estimates.\n", "Weir and Cockerham mean Fst estimate: 0.0029054\n", "Weir and Cockerham weighted Fst estimate: 0.14582\n", "After filtering, kept 120130 out of a possible 120130 Sites\n", "Run Time = 25.00 seconds\n", "\n", "real\t0m24.933s\n", "user\t0m0.760s\n", "sys\t0m13.630s\n" ] } ], "source": [ "%%bash\n", "time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\n", "mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_NF.fst" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1HL vs. 1SN" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "VCFtools - 0.1.14\n", "(C) Adam Auton and Anthony Marcketta 2009\n", "\n", "Parameters as interpreted:\n", "\t--vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "Eighth Header entry should be INFO: INFO \n", "Keeping individuals in 'keep' list\n", "After filtering, kept 64 out of 96 Individuals\n", "Outputting Weir and Cockerham Fst estimates.\n", "Weir and Cockerham mean Fst estimate: 0.018513\n", "Weir and Cockerham weighted Fst estimate: 0.18011\n", "After filtering, kept 120130 out of a possible 120130 Sites\n", "Run Time = 24.00 seconds\n", "\n", "real\t0m24.362s\n", "user\t0m0.800s\n", "sys\t0m13.780s\n" ] } ], "source": [ "%%bash\n", "time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_SN.fst" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1NF vs 1SN" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "VCFtools - 0.1.14\n", "(C) Adam Auton and Anthony Marcketta 2009\n", "\n", "Parameters as interpreted:\n", "\t--vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "Eighth Header entry should be INFO: INFO \n", "Keeping individuals in 'keep' list\n", "After filtering, kept 64 out of 96 Individuals\n", "Outputting Weir and Cockerham Fst estimates.\n", "Weir and Cockerham mean Fst estimate: -0.010855\n", "Weir and Cockerham weighted Fst estimate: 0.10355\n", "After filtering, kept 120130 out of a possible 120130 Sites\n", "Run Time = 27.00 seconds\n", "\n", "real\t0m26.961s\n", "user\t0m1.890s\n", "sys\t0m12.430s\n" ] } ], "source": [ "%%bash\n", "time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1NF_1SN.fst" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### 1HL vs. 1NF vs. 1SN" ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "VCFtools - 0.1.14\n", "(C) Adam Auton and Anthony Marcketta 2009\n", "\n", "Parameters as interpreted:\n", "\t--vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\t--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop\n", "\t--keep /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "Eighth Header entry should be INFO: INFO \n", "Keeping individuals in 'keep' list\n", "After filtering, kept 96 out of 96 Individuals\n", "Outputting Weir and Cockerham Fst estimates.\n", "Weir and Cockerham mean Fst estimate: 0.048516\n", "Weir and Cockerham weighted Fst estimate: 0.13739\n", "After filtering, kept 120130 out of a possible 120130 Sites\n", "Run Time = 25.00 seconds\n", "\n", "real\t0m24.840s\n", "user\t0m1.080s\n", "sys\t0m13.720s\n" ] } ], "source": [ "%%bash\n", "time vcftools --vcf /root/data/20161117_oly_gbs_vcf_analysis/oly_gbs_pyrad.vcf \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1HL.pop \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1NF.pop \\\n", "--weir-fst-pop /root/data/20161117_oly_gbs_vcf_analysis/1SN.pop\n", "\n", "mv out.weir.fst /root/data/20161117_oly_gbs_vcf_analysis/1HL_1NF_1SN.fst" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.2" } }, "nbformat": 4, "nbformat_minor": 1 }