Hi
I'm trying to use Haplotype Caller for some WES and I used the --emitRefConfidence GVCF option in order to see only variants in my VCF output (no 0/0 homo wild type). Unexpectedly I obtained something like this:
[...]
chrX 155254672 . C . . END=155254791 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
chrX 155254853 . T . . END=155254972 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
What am I getting wrong?
