Feature request: add counts for individuals with a specific variant

scholl-lab / vcf-filtering

A collection of scripts for filtering annotated variant call format files

MIT License

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Closed berntpopp closed 1 week ago

berntpopp commented 1 month ago

Add a column with the number of individuals who have a ceratin genotype (0/1 vs 1/1, and maybe 0/0 if gVCF)

berntpopp commented 3 weeks ago

Also count the toal number of individuals or alleles (e.g. 0/0, 01,, 1/1).

CAVE: the currently merged VCFs are set to 0/0 instead of ./. if no call was present. So this will always result in the cohort size.