jts
commented
6 months ago Perhaps you meant to ask this in the freebayes repository, not here?
On Wed, Apr 3, 2024 at 5:32 AM emilydolivo97 @.***> wrote:
Hello , I applied freebayes to my different samples, generated a VCF file, and annotated it. I would like to know how I can determine the frequency of each variant per sample.
this is how my vcf file looks like :
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sxxxxxxxx9.fastq
Sxxxxxxxx8.fastq Sxxxxxxxx3.fastq Sxxxxxxxx0.fastq Sxxxxxxx10.fastq Sxxxxxxx49.fastq Sxxxxxxxx5.fastq Sxxxxxxxx2.fastq Sxxxxxxxx7.fastq Sxxxxxxxx1.fastq Sxxxxxx341.fastq Sxxxxxx746.fastq Sxxxxxx887.fastq Sxxxxxxx72.fastq Sxxxxxx413.fastq Sxxxxxxx08.fastq Sxxxxxx494.fastq Sxxxxxxx84.fastq DLXXXXX.4 687 . C T 4.38287e-13 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=39;CIGAR=1X;DP=2179;DPB=2179;DPRA=0.986735;EPP=63.6445;EPPR=370.696;GTI=0;LEN=1;MEANALT=1.75;MQM=60;MQMR=59.9722;NS=18;NUMALT=1;ODDS=135.142;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=259;QR=40628;RO=2119;RPL=0;RPP=87.6977;RPPR=4604.36;RPR=39;RUN=1;SAF=3;SAP=63.6445;SAR=36;SRF=760;SRP=370.696;SRR=1359;TYPE=snp;technology.Nanopore=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:121:119,1:119:2436:1:6:0,-35.5636,-218.82 0/0:136:130,5:130:2349:5:32:0,-37.7391,-208.61 0/0:116:114,2:114:2317:2:7:0,-34.2545,-208.029 0/0:118:112,6:112:2005:6:35:0,-32.3132,-176.731 0/0:127:124,2:124:2482:2:8:0,-37.2564,-222.749 0/0:113:111,2:111:1995:2:12:0,-32.8764,-178.568 0/0:126:125,0:125:2498:0:0:0,-37.6287,-224.944 0/0:135:129,4:129:2247:4:16:0,-38.587,-200.899 0/0:131:129,1:129:2527:1:9:0,-38.3089,-226.709 0/0:107:103,1:103:2029:1:12:0,-30.2088,-181.628 0/0:125:122,2:122:2064:2:21:0,-35.4144,-183.924 0/0:105:102,1:102:2034:1:10:0,-30.0894,-182.259 0/0:119:116,1:116:2262:1:12:0,-34.1188,-202.579 0/0:119:117,0:117:2379:0:0:0,-35.2205,-214.238 0/0:124:120,3:120:2347:3:15:0,-35.6842,-209.993 0/0:124:119,3:119:2538:3:28:0,-34.1737,-225.986 0/0:119:117,2:117:2089:2:15:0,-34.3976,-186.748 0/0:114:110,3:110:2030:3:21:0,-32.0964,-180.914 DLXXXXX.4 688 . T C 0 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=139;CIGAR=1X;DP=2122;DPB=2122;DPRA=0;EPP=216.861;EPPR=211.476;GTI=0;LEN=1;MEANALT=1.77778;MQM=60;MQMR=59.9424;NS=18;NUMALT=1;ODDS=117.062;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=922;QR=30518;RO=1962;RPL=0;RPP=304.845;RPPR=4263.44;RPR=139;RUN=1;SAF=11;SAP=216.861;SAR=128;SRF=764;SRP=211.476;SRR=1198;TYPE=snp;technology.Nanopore=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:118:110,7:110:1816:7:66:0,-29.2509,-157.556 0/0:129:118,11:118:1771:11:74:0,-32.1056,-152.785 0/0:112:103,8:103:1774:8:56:0,-28.3743,-154.704 0/0:112:102,9:102:1387:9:56:0,-28.3903,-119.483 0/0:125:118,5:118:1862:5:36:0,-33.7889,-164.406 0/0:112:100,10:100:1416:10:65:0,-27.28,-121.655 0/0:124:118,6:118:1846:6:33:0,-34.3027,-163.038 0/0:130:117,11:117:1679:11:62:0,-33.0099,-145.591 0/0:129:121,8:121:1809:8:52:0,-34.0879,-158.206 0/0:106:101,3:101:1478:3:22:0,-29.3011,-131.116 0/0:117:111,6:111:1541:6:51:0,-30.5455,-134.141 0/0:100:95,5:95:1575:5:35:0,-26.883,-138.685 0/0:116:112,4:112:1792:4:26:0,-32.5145,-159.016 0/0:118:112,5:112:1813:5:27:0,-32.7788,-160.836 0/0:122:107,11:107:1867:11:75:0,-28.7803,-161.359 0/0:123:115,7:115:1920:7:44:0,-32.7719,-168.922 0/0:116:105,8:105:1632:8:56:0,-28.9958,-141.906 0/0:113:97,15:97:1540:15:86:0,-26.0529,-130.944
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emilydolivo97
Hello , I applied freebayes to my different samples, generated a VCF file, and annotated it. I would like to know how I can determine the frequency of each variant per sample.
this is how my vcf file looks like :
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sxxxxxxxx9.fastq Sxxxxxxxx8.fastq Sxxxxxxxx3.fastq Sxxxxxxxx0.fastq Sxxxxxxx10.fastq Sxxxxxxx49.fastq Sxxxxxxxx5.fastq Sxxxxxxxx2.fastq Sxxxxxxxx7.fastq Sxxxxxxxx1.fastq Sxxxxxx341.fastq Sxxxxxx746.fastq Sxxxxxx887.fastq Sxxxxxxx72.fastq Sxxxxxx413.fastq Sxxxxxxx08.fastq Sxxxxxx494.fastq Sxxxxxxx84.fastq
DLXXXXX.4 687 . C T 4.38287e-13 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=39;CIGAR=1X;DP=2179;DPB=2179;DPRA=0.986735;EPP=63.6445;EPPR=370.696;GTI=0;LEN=1;MEANALT=1.75;MQM=60;MQMR=59.9722;NS=18;NUMALT=1;ODDS=135.142;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=259;QR=40628;RO=2119;RPL=0;RPP=87.6977;RPPR=4604.36;RPR=39;RUN=1;SAF=3;SAP=63.6445;SAR=36;SRF=760;SRP=370.696;SRR=1359;TYPE=snp;technology.Nanopore=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:121:119,1:119:2436:1:6:0,-35.5636,-218.82 0/0:136:130,5:130:2349:5:32:0,-37.7391,-208.61 0/0:116:114,2:114:2317:2:7:0,-34.2545,-208.029 0/0:118:112,6:112:2005:6:35:0,-32.3132,-176.731 0/0:127:124,2:124:2482:2:8:0,-37.2564,-222.749 0/0:113:111,2:111:1995:2:12:0,-32.8764,-178.568 0/0:126:125,0:125:2498:0:0:0,-37.6287,-224.944 0/0:135:129,4:129:2247:4:16:0,-38.587,-200.899 0/0:131:129,1:129:2527:1:9:0,-38.3089,-226.709 0/0:107:103,1:103:2029:1:12:0,-30.2088,-181.628 0/0:125:122,2:122:2064:2:21:0,-35.4144,-183.924 0/0:105:102,1:102:2034:1:10:0,-30.0894,-182.259 0/0:119:116,1:116:2262:1:12:0,-34.1188,-202.579 0/0:119:117,0:117:2379:0:0:0,-35.2205,-214.238 0/0:124:120,3:120:2347:3:15:0,-35.6842,-209.993 0/0:124:119,3:119:2538:3:28:0,-34.1737,-225.986 0/0:119:117,2:117:2089:2:15:0,-34.3976,-186.748 0/0:114:110,3:110:2030:3:21:0,-32.0964,-180.914 DLXXXXX.4 688 . T C 0 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=139;CIGAR=1X;DP=2122;DPB=2122;DPRA=0;EPP=216.861;EPPR=211.476;GTI=0;LEN=1;MEANALT=1.77778;MQM=60;MQMR=59.9424;NS=18;NUMALT=1;ODDS=117.062;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=922;QR=30518;RO=1962;RPL=0;RPP=304.845;RPPR=4263.44;RPR=139;RUN=1;SAF=11;SAP=216.861;SAR=128;SRF=764;SRP=211.476;SRR=1198;TYPE=snp;technology.Nanopore=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:118:110,7:110:1816:7:66:0,-29.2509,-157.556 0/0:129:118,11:118:1771:11:74:0,-32.1056,-152.785 0/0:112:103,8:103:1774:8:56:0,-28.3743,-154.704 0/0:112:102,9:102:1387:9:56:0,-28.3903,-119.483 0/0:125:118,5:118:1862:5:36:0,-33.7889,-164.406 0/0:112:100,10:100:1416:10:65:0,-27.28,-121.655 0/0:124:118,6:118:1846:6:33:0,-34.3027,-163.038 0/0:130:117,11:117:1679:11:62:0,-33.0099,-145.591 0/0:129:121,8:121:1809:8:52:0,-34.0879,-158.206 0/0:106:101,3:101:1478:3:22:0,-29.3011,-131.116 0/0:117:111,6:111:1541:6:51:0,-30.5455,-134.141 0/0:100:95,5:95:1575:5:35:0,-26.883,-138.685 0/0:116:112,4:112:1792:4:26:0,-32.5145,-159.016 0/0:118:112,5:112:1813:5:27:0,-32.7788,-160.836 0/0:122:107,11:107:1867:11:75:0,-28.7803,-161.359 0/0:123:115,7:115:1920:7:44:0,-32.7719,-168.922 0/0:116:105,8:105:1632:8:56:0,-28.9958,-141.906 0/0:113:97,15:97:1540:15:86:0,-26.0529,-130.944