Hi GATK team,
When I checked closely by IGV, I found many of the loci, with all reads supporting variants, were reported as a HET genotype by HC.
After go back to the VCF result, I still don't understand why HC called this as a HET genotype, due to the ref's AD is 0, for example:
0/1:0,20:99:1069,0,1743
The whole line of this loci in VCF as below:
SCF1 47255 . T A 21688.96 . AC=33;AF=0.500;AN=66;ActiveRegionSize=225;DP=264;EVENTLENGTH=0;FS=0.000;Haploty
peScore=73.8674;InbreedingCoeff=-0.8774;MLEAC=33;MLEAF=0.500;MQ=85.46;MQ0=0;NVH=5;NumHapAssembly=19;NumHapEval=12;QD=84.07;QDE=16.81;TYPE=SNP;extType=S
NP GT:AD:GQ:PL 1/1:0,4:18:503,18,0 0/1:0,16:99:1732,0,2964 0/1:0,4:99:279,0,173 0/1:0,5:99:353,0,884 0/1:0,3:99:279,0,645 0/1:0
,4:99:270,0,584 0/1:0,19:99:1428,0,4290 0/1:0,7:99:388,0,794 0/1:0,3:99:302,0,391 0/1:0,15:99:1087,0,1165 0/1:0,6:99:529,0,1437 0/1:0,4:99:4
82,0,493 0/1:0,12:99:1245,0,2556 0/1:0,5:99:433,0,605 0/1:0,4:99:624,0,1135 0/1:0,3:99:362,0,1219 0/1:0,4:99:454,0,866 0/1:0,5:99:200,0,29
8 0/1:0,14:99:1846,0,1785 0/1:0,3:99:130,0,205 0/1:0,16:99:1453,0,999 0/1:0,15:99:757,0,866 0/1:0,12:99:939,0,518 0/1:0,10:99:697,0,758 0/
1:0,8:99:790,0,1319 0/1:0,9:99:748,0,1417 0/1:0,7:99:634,0,2198 0/0:0,6:63:0,63,1438 0/1:0,8:99:1029,0,1634 0/1:0,5:99:676,0,874 0/1:0,2:6
5:65,0,107 0/1:0,20:99:1069,0,1743 0/1:0,2:14:14,0,710
Best, SK