Entering edit mode
4.5 years ago
BAGeno
▴
190
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.
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?