In the second sample, GT is 0/0 and FT is HomRef, however PL is 24,0,112, and SR is 3 for the variant allele. There seems to be conflict between GT/FT and PL/SR. Which should I believe?
The values are not in conflict -- the genotype assignments are not taken directly from the likelihoods (PLs)-- the GT and FT values here reflect the final genotype posterior, including the prior.
I've run Manta on a WGS sample and one of the called variants was labelled as "HomRef" in the FT field in one sample:
In the second sample, GT is 0/0 and FT is HomRef, however PL is 24,0,112, and SR is 3 for the variant allele. There seems to be conflict between GT/FT and PL/SR. Which should I believe?
Thanks,