Entering edit mode
7.6 years ago
arnaud.capron
•
0
I've been analyzing GBS data for a fungus (haploid) and I'm puzzled by some of the genotype calls I get in the VCF. For example:
GT:PL:DP:GQ ./.:0,255,255:233:99
Why is no genotype given (GT) while PL is 0,255,255? Shouldn't this position be 0/0?
From the same individual is have 0/0:0,255,224:141:99 a few positions down and another individual at the same position show 0/0:0,33,127:11:99.
I'm using VCFTools to filter the .bcf
Yep, that was the high coverage filter (--max-DP 200). Thanks!