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AD value after GenotypeGVCFs
I run HC for several samples, then I run GenotypeGVCFs to merge all gVCF files. (I'm using version 3.1.1)
I've noticed that for some variations, although there are only 2 alleles, the AD values for all samples contain information for multiple alleles.
For example: '0,83,0,0,0' for homozygous or '11,40,0,0,0' for heterozygous.
Below is the complete line:
chr15 82637079 . C T 91046.53 . AC=26;AF=0.867;AN=30;BaseQRankSum=-1.146e+00;ClippingRankSum=2.25;DP=2139;FS=0.000;InbreedingCoeff=-0.1588;MLEAC=26;MLEAF=0.867;MQ=39.29;MQ0=0;MQRankSum=2.18;QD=30.88;ReadPosRankSum=0.174 GT:AD:DP:GQ:PL 1/1:0,23,0,0,0:23:77:1081,77,0 0/1:11,40,0,0,0:51:99:1688,0,473 1/1:1,320,0,0,0:321:99:14836,972,0 1/1:2,168,0,0,0:170:99:7466,471,0 0/1:23,205,0,0,0:228:99:8646,0,649 ./.:.:3 1/1:0,3,0,0,0:3:9:135,9,0 1/1:0,139,0,0,0:139:99:6349,427,0 1/1:0,83,0,0,0:83:99:4251,307,0 0/1:7,60,0,0,0:67:99:2748,0,310 0/1:6,38,0,0,0:44:99:1921,0,124 1/1:0,294,0,0,0:294:99:15437,1085,0 1/1:0,67,0,0,0:67:99:3557,253,0 1/1:0,105,0,0,0:105:99:5289,362,0 1/1:0,243,0,0,0:243:99:11587,810,0 1/1:0,257,0,0,0:257:99:11929,821,0
Any suggestion how should I interpret this values?
Thank you for your help,