I've created GVCFs using the WholeGenomeGermlineSingleSample_v3.0.0 workflow, and then processed these with CombineGVCFs and GenotypeGVCFs, all with default settings ("Functional Equivalence" version for the first step).
I’ve run into this behavior that very many of the sites with appreciable read depth (say > 20X) and 100% reference reads are being called as “./.” instead of “0/0”. I’m just running things with default settings, so I wouldn’t think these are being filtered in some way.
Here is an example of what I mean, based on a test with 4 samples
chr1 63643 . A G 90 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.63;DP=109;ExcessHet=4.7712;FS=2.766;MLEAC=2;MLEAF=0.500;MQ=22.46;MQRankSum=-6.030e-01;QD=1.80;ReadPosRankSum=1.51;SOR=1.329 GT:AD:DP:GQ:PL 0/1:10,5:15:29:57,0,29 0/1:26,9:35:29:45,0,29 ./.:29,0:29:40 ./.:30,0:30:40
the last two samples have read depth of 29 and 30, but are set to ./.
I’d prefer to have these called as “0/0” for a number of reasons. Any ideas of how to change this behavior?