Counting allele counts/frequencies from a vcf file with both cases and controls

Question

[tacrolimus]

Dear Biostars members,

I a multi-sample vcf which has been annotated with VEP. The vcf has both cases and controls. I would like to know the allele counts and frequencies for cases vs controls.

I am able to use bcftools to pull the relevant fields but was wondering if there was a way of feeding it a case control label and it giving me a split of the results based from this rather than dividing the vcf into cases and controls and then running the analysis separately?

Many thanks for your time

[Ram]

You can create 2 one-sample-ID-per-line files of case IDs and control IDs and use them with the -S parameter available in many bcftools sub-tools.

Answer 1

[Paolo]

This is the aim of https://pcingola.github.io/SnpEff/ss_casecontrol/