missing genotype ./. even with many reads under AD and DP

missing genotype ./. even with many reads under AD and DP


Hi All,

I am trying to troubleshoot all the missing genotypes in my VCF. I don’t quite understand why I get missing genotypes (./.) when there are plenty of reads under AD and DP.
I think it’s because the GQ also appear to be 0. Can someone confirm this or shed some light on what’s going on please.

I copied some lines from the raw genotyped VCF. I used GATK4 Haplotypecaller for variant calling > CombinedGVCFs > GenotypeGVCF

PHUM306900 10716 . C T 210835.07 . AC=435;AF=0.867;AN=502;BaseQRankSum=0.654;DP=13029;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4908;MLEAC=755;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=31.27;ReadPosRankSum=1.10;SOR=0.781 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,52:52:99:1|1:10716_C_T:2252,156,0:10716 0|1:15,10:25:99:0|1:10716_C_T:375,0,600:10716 ./.:19,0:19:.:.:.:0,0,0 ./.:26,0:26:.:.:.:0,0,0

I should add that I already tried using FixVcfMissingGenotypes and it didn’t change any calls on the samples I tried.
Any insight would be much appreciated.




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