Problem with allele frequency calculation in vcf
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Entering edit mode
17 months ago
BAGeno ▴ 180

Hi,

I am encountering problem in vcf related to allele frequency. Here is my sample file.

chr1    113834946   rs2476601   A   G,T 938986  PASS    AC=21,1;AF=0.983315,0.000538213;AN=22;BaseQRankSum=1.13;ClippingRankSum=0.217;DP=33382;ExcessHet=4.0054;FS=0;InbreedingCoeff=-0.0158;MLEAC=1897,1;MLEAF=0.984,0.0005187;MQ=25.78;MQRankSum=0.253;POSITIVE_TRAIN_SITE;QD=28.3;ReadPosRankSum=0.638;SOR=0.773;VQSLOD=5.18;culprit=QD;VQSRMODE=SNP;NS=929;ExcHet=1,0;AA_chimp=G;AA_ensembl=G   GT:AD:DP:GQ:PGT:PID:PL  1/1:0,35,0:35:99:.:.:1263,105,0,1263,.,1263 1/1:0,37,0:37:99:.:.:1389,111,0,1389,.,1389 1/1:0,28,0:28:84:.:.:1001,84,0,1001,.,1001  1/2:0,17,19:36:99:.:.:1209,618,566,591,.,534    1/1:1,48,0:49:99:.:.:1253,137,0,1255,.,1262 1/1:0,23,0:23:69:.:.:823,69,0,823,.,823 1/1:0,39,0:39:99:.:.:1004,117,0,1004,.,1004 1/1:0,36,0:36:99:.:.:963,108,0,963,.,963    1/1:0,40,0:40:99:.:.:1035,119,0,1035,.,1035 1/1:0,33,0:33:99:.:.:1161,99,0,1161,.,1161  1/1:0,51,0:51:99:.:.:1310,153,0,1310,.,1310
chr1    159714875   rs3091244   G   A,T 282302  PASS    AC=5,0;AF=0.215517,0.134159;AN=22;BaseQRankSum=0.54;ClippingRankSum=0.158;DP=33578;ExcessHet=1.3102;FS=0.53;InbreedingCoeff=0.0201;MLEAC=417,262;MLEAF=0.216,0.136;MQ=19.76;MQRankSum=0.029;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=0.402;SOR=0.649;VQSLOD=4.68;culprit=MQ;VQSRMODE=SNP;NS=928;ExcHet=1,0;AA_chimp=G;AA_ensembl=G   GT:AD:DP:GQ:PGT:PID:PL  0/1:14,15,0:29:99:.:.:455,0,396,496,.,937   0/0:41,1,1:42:99:.:.:0,105,1575,105,.,1575  0/1:16,21,0:37:99:.:.:688,0,506,736,.,1305  0/1:17,17,0:34:99:.:.:528,0,497,579,.,1127  0/0:33,0,0:33:87:.:.:0,87,1305,87,.,1305    0/1:19,25,0:44:99:.:.:752,0,492,808,.,1375  0/1:20,14,0:34:99:.:.:258,0,413,318,.,773   0/0:43,0,0:43:99:.:.:0,120,1800,120,.,1800  0/0:29,1,1:30:75:.:.:0,75,1326,75,.,1326    0/0:44,0,0:44:99:.:.:0,120,1800,120,.,1800  0/0:47,1,1:48:99:.:.:0,120,1800,120,.,1800

Allele frequency is not computed properly as allele count divided by allele number does not equal to values mentioned in AF. Any idea what is causing this and how to solve this problem.

vcf allele frequency • 377 views
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Entering edit mode

You should ask this on the GATK forums. I think it has something to do with the ploidy of your sample.

edit: Just making sure, your variants were called with GATK4?

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