QUAL in vcf seems the variant count?

lh3 / minipileup

Simple pileup-based variant caller

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QUAL in vcf seems the variant count? #13

Closed baozg closed 3 months ago

baozg commented 3 months ago

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 3 months ago

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