Question: Problem with allele frequency calculation in vcf
1
gravatar for BAGeno
6 weeks ago by
BAGeno160
BAGeno160 wrote:

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.

allele frequency vcf • 106 views
ADD COMMENTlink written 6 weeks ago by BAGeno160

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?

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Amar620
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