lh3/minipileup

QUAL in vcf seems the variant count?

baozg opened this issue · 1 comments

baozg commented

Hi, @lh3

I am using minipileup for counting alleles in the whole genome alignment with minimap2. The QUAL field of output vcf seems the non-ref individual count from pileup format, is that correct?

lh3 commented

Yes, it is. Minipileup doesn't output proper QUAL.