The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Project level VCF
I am combining gVCFs that are processed exactly the same, I observed that most variants have this tag: "GT:AD:DP:GQ:PL". However for some variants, within the same variant, they can have this tag GT:AD:DP:GQ:PGT:PID:PL" for some of the samples but not others.
I did some testing
a) perform combineGVCF on a set of gVCF then do genotypeGVCF (test a)
b) perform genotypeGVCF only on this set of gVCF (test b)
What I observed is that there are some variants present only in test a, but not in test b. Same thing happens vice versa, i.e. variants present only in test b, but not in test a. These kind of variants all all got the same tag GT:AD:DP:GQ:PGT:PID:PL. Why is this the case? And what is combineGVCF and genotypeGVCF actually doing?