frequency of each variant per sample

[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 4.38769E-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;ANN=T|missense_variant|MODERATE|NAD9|Gene_190_750|transcript|ABF29491.1|protein_coding|1/1|c.497C>T|p.Pro166Leu|497/561|497/561|166/186||,T|upstream_gene_variant|MODIFIER|PvRXLR|Gene_818_1972|transcript|ABF29492.1|protein_coding||c.-132C>T|||||132|,T|upstream_gene_variant|MODIFIER|NAD5|Gene_2075_2280|transcript|ABF29493.1|protein_coding||c.-1389C>T|||||1389|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:AD:RO:QR:AO:QA:GL 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 0/0:125:122,2:122:2064:2:21:0,-35.4144,-183.924 0/0:119:117,2:117:2089:2:15:0,-34.3976,-186.748 0/0:105:102,1:102:2034:1:10:0,-30.0894,-182.259 0/0:136:130,5:130:2349:5:32:0,-37.7391,-208.61 0/0:107:103,1:103:2029:1:12:0,-30.2088,-181.628 0/0:124:119,3:119:2538:3:28:0,-34.1737,-225.986 0/0:119:116,1:116:2262:1:12:0,-34.1188,-202.579 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 0/0:114:110,3:110:2030:3:21:0,-32.0964,-180.914 0/0:119:117,0:117:2379:0:0:0,-35.2205,-214.238 0/0:135:129,4:129:2247:4:16:0,-38.587,-200.899 0/0:121:119,1:119:2436:1:6:0,-35.5636,-218.82 0/0:131:129,1:129:2527:1:9:0,-38.3089,-226.709 0/0:124:120,3:120:2347:3:15:0,-35.6842,-209.993

DLXXXXX.4 688 . T C 0.0 . 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;ANN=C|synonymous_variant|LOW|NAD9|Gene_190_750|transcript|ABF29491.1|protein_coding|1/1|c.498T>C|p.Pro166Pro|498/561|498/561|166/186||,C|upstream_gene_variant|MODIFIER|PvRXLR|Gene_818_1972|transcript|ABF29492.1|protein_coding||c.-131T>C|||||131|,C|upstream_gene_variant|MODIFIER|NAD5|Gene_2075_2280|transcript|ABF29493.1|protein_coding||c.-1388T>C|||||1388|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:AD:RO:QR:AO:QA:GL 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 0/0:117:111,6:111:1541:6:51:0,-30.5455,-134.141 0/0:116:105,8:105:1632:8:56:0,-28.9958,-141.906 0/0:100:95,5:95:1575:5:35:0,-26.883,-138.685 0/0:129:118,11:118:1771:11:74:0,-32.1056,-152.785 0/0:106:101,3:101:1478:3:22:0,-29.3011,-131.116 0/0:123:115,7:115:1920:7:44:0,-32.7719,-168.922 0/0:116:112,4:112:1792:4:26:0,-32.5145,-159.016 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 0/0:113:97,15:97:1540:15:86:0,-26.0529,-130.944 0/0:118:112,5:112:1813:5:27:0,-32.7788,-160.836 0/0:130:117,11:117:1679:11:62:0,-33.0099,-145.591 0/0:118:110,7:110:1816:7:66:0,-29.2509,-157.556 0/0:129:121,8:121:1809:8:52:0,-34.0879,-158.206 0/0:122:107,11:107:1867:11:75:0,-28.7803,-161.359

DLXXXXX.4 689 . G A 7.66643E-14 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=80;CIGAR=1X;DP=2172;DPB=2172;DPRA=0;EPP=60.4457;EPPR=363.926;GTI=0;LEN=1;MEANALT=2.61111;MQM=60;MQMR=59.944;NS=18;NUMALT=2;ODDS=113.649;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=491;QR=31152;RO=2017;RPL=0;RPP=176.728;RPPR=4382.87;RPR=80;RUN=1;SAF=63;SAP=60.4457;SAR=17;SRF=719;SRP=363.926;SRR=1298;TYPE=snp;technology.Nanopore=1;ANN=A|missense_variant|MODERATE|NAD9|Gene_190_750|transcript|ABF29491.1|protein_coding|1/1|c.499G>A|p.Val167Ile|499/561|499/561|167/186||,A|upstream_gene_variant|MODIFIER|PvRXLR|Gene_818_1972|transcript|ABF29492.1|protein_coding||c.-130G>A|||||130|,A|upstream_gene_variant|MODIFIER|NAD5|Gene_2075_2280|transcript|ABF29493.1|protein_coding||c.-1387G>A|||||1387|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:108,6:108:1864:6:35:0,-31.2324,-164.69 0/0:112:102,1:102:1407:1:6:0,-30.4676,-125.625 0/0:130:125,4:125:1886:4:25:0,-36.6049,-167.56 0/0:121:115,2:115:1587:2:21:0,-33.3197,-140.985 0/0:120:111,6:111:1620:6:35:0,-32.1183,-142.706 0/0:103:95,4:95:1533:4:23:0,-27.7357,-135.986 0/0:132:119,8:119:1850:8:39:0,-34.7647,-163.049 0/0:110:96,8:96:1450:8:50:0,-26.8143,-126.069 0/0:132:121,3:121:1993:3:12:0,-36.2692,-178.336 0/0:119:109,6:109:1723:6:32:0,-31.8144,-152.233 0/0:114:106,4:106:1526:4:18:0,-31.5246,-135.78 0/0:121:116,2:116:1825:2:9:0,-34.7402,-161.873 0/0:114:103,7:103:1532:7:74:0,-26.4452,-131.259 0/0:120:115,3:115:1840:3:31:0,-32.6906,-162.883 0/0:133:122,6:122:1906:6:20:0,-36.7747,-169.812 0/0:120:114,2:114:1884:2:5:0,-34.4911,-169.191 0/0:133:121,7:121:1785:7:50:0,-34.0334,-156.212 0/0:122:119,1:119:1941:1:6:0,-35.5786,-174.246

DLXXXXX.4 689 . G C 7.66643E-14 . AB=0;ABP=0;AC=0;AF=0;AN=36;AO=59;CIGAR=1X;DP=2172;DPB=2172;DPRA=0;EPP=98.7391;EPPR=363.926;GTI=0;LEN=1;MEANALT=2.61111;MQM=60;MQMR=59.944;NS=18;NUMALT=2;ODDS=113.649;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=602;QR=31152;RO=2017;RPL=0;RPP=131.127;RPPR=4382.87;RPR=59;RUN=1;SAF=4;SAP=98.7391;SAR=55;SRF=719;SRP=363.926;SRR=1298;TYPE=snp;technology.Nanopore=1;ANN=C|missense_variant|MODERATE|NAD9|Gene_190_750|transcript|ABF29491.1|protein_coding|1/1|c.499G>C|p.Val167Leu|499/561|499/561|167/186||,C|upstream_gene_variant|MODIFIER|PvRXLR|Gene_818_1972|transcript|ABF29492.1|protein_coding||c.-130G>C|||||130|,C|upstream_gene_variant|MODIFIER|NAD5|Gene_2075_2280|transcript|ABF29493.1|protein_coding||c.-1387G>C|||||1387|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:AD:RO:QR:AO:QA:GL 0/0:116:108,2:108:1864:2:29:0,-30.4817,-165.225 0/0:112:102,7:102:1407:7:57:0,-27.665,-121.037 0/0:130:125,1:125:1886:1:9:0,-37.1143,-168.997 0/0:121:115,2:115:1587:2:20:0,-33.4122,-141.075 0/0:120:111,2:111:1620:2:28:0,-31.4799,-143.332 0/0:103:95,2:95:1533:2:11:0,-28.212,-137.064 0/0:132:119,4:119:1850:4:40:0,-33.4161,-162.954 0/0:110:96,5:96:1450:5:42:0,-26.6151,-126.785 0/0:132:121,7:121:1993:7:91:0,-30.2847,-171.225 0/0:119:109,4:109:1723:4:72:0,-27.4863,-148.627 0/0:114:106,3:106:1526:3:33:0,-29.822,-134.428 0/0:121:116,1:116:1825:1:10:0,-34.3175,-161.782 0/0:114:103,3:103:1532:3:34:0,-28.8445,-134.857 0/0:120:115,2:115:1840:2:7:0,-34.6178,-165.044 0/0:133:122,5:122:1906:5:56:0,-33.1551,-166.568 0/0:120:114,4:114:1884:4:36:0,-32.2382,-166.401 0/0:133:121,3:121:1785:3:18:0,-35.7119,-159.09 0/0:122:119,2:119:1941:2:9:0,-35.6246,-173.977

[lindenb]

cross-posted: https://www.biostars.org/p/9591687/

[emilydolivo97]

cross-posted: https://www.biostars.org/p/9591687/

yess , because I need a quick answer .
So could you please help me with that and confirm if what they said in the publication is correct or not.
Does my question "frequency of each variant per sample" make sense tu you ?