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