Strange Allele Frequency in vcf file
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Entering edit mode
20 months ago
GP_PG • 0

Hi everyone. I performed a snp calling using GATK and following all the suggestions in the BestPractices sections. I performed single snp calling for two samples using HaplotypeCaller with the -ERC GVCF option and then performed the joint calling with GenotypeGVCFs. The vcf i get has a strange AF with "fixed" values of 0.25, 0.5 or 1 and i don't understand if this is correct. Could you help me? here's a small piece of the vcf file:

NC_023046.1 3209997 .   T   G   1819.46 .   AC=2;AF=0.500;AN=4;BaseQRankSum=1.00;ClippingRankSum=0.00;DP=139;ExcessHet=4.7712;FS=3.345;MLEAC=2;MLEAF=0.500;MQ=43.30;MQRankSum=0.00;QD=14.56;RAW_MQ=260624.00;ReadPosRankSum=0.00;SOR=1.044  GT:AD:DP:GQ:PGT:PID:PL  0/1:24,23:47:99:0|1:3209964_C_T:894,0,917   0/1:52,26:78:99:.:.:935,0,2085
NC_023046.1 3210002 .   G   C   3436.46 .   AC=2;AF=0.500;AN=4;BaseQRankSum=1.00;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=43.35;MQRankSum=1.00;QD=30.96;RAW_MQ=259328.00;ReadPosRankSum=0.00;SOR=0.650  GT:AD:DP:GQ:PL  0/1:14,29:46:99:1176,0,501  0/1:13,55:77:99:2270,0,380
NC_023046.1 3210003 .   A   T   3985.46 .   AC=2;AF=0.500;AN=4;BaseQRankSum=1.00;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=43.35;MQRankSum=0.00;QD=32.67;RAW_MQ=259328.00;ReadPosRankSum=0.00;SOR=0.733  GT:AD:DP:GQ:PL  0/1:14,32:46:99:1302,0,492  0/1:12,64:77:99:2693,0,308
NC_023046.1 3210009 .   C   T   159.23  .   AC=1;AF=0.250;AN=4;BaseQRankSum=1.00;ClippingRankSum=0.00;DP=140;ExcessHet=3.0103;FS=6.531;MLEAC=1;MLEAF=0.250;MQ=53.24;MQRankSum=0.00;QD=2.02;RAW_MQ=263653.00;ReadPosRankSum=0.00;SOR=1.350   GT:AD:DP:GQ:PGT:PID:PL  0/0:44,3:47:6:0|1:3209964_C_T:0,6,1845  0/1:70,9:79:99:.:.:167,0,2912
NC_023046.1 3210013 .   C   T   497.46  .   AC=2;AF=0.500;AN=4;BaseQRankSum=0.00;ClippingRankSum=0.00;DP=138;ExcessHet=4.7712;FS=8.481;MLEAC=2;MLEAF=0.500;MQ=43.46;MQRankSum=-1.000e+00;QD=4.01;RAW_MQ=260611.00;ReadPosRankSum=0.00;SOR=1.721 GT:AD:DP:GQ:PGT:PID:PL  0/1:42,5:47:84:0|1:3209964_C_T:84,0,1749    0/1:62,15:77:99:.:.:423,0,2487
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Entering edit mode

You have 2 diploid samples, so that's 4 alleles. The only possible AF values in mutant loci are 1/4 (0.25), 2/4 (0.5), 3/4 (0.75) and 4/4 (1). What you are seeing is expected.

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