Hi, I have 3 VCF files with no overlapping samples but with overlapping variants. I’d like to subset the 3 VCFs to only have the common variants and then merge them to create a large VCF with all the samples from the 3 VCFs or have a merged VCF outputted.
I’ve tried to use bcftools isec, but it only prints the list of sites. It has a note that i haven’t included a -w option. Can bcftools isec produced the subsetted VCFs or is there another tool I should use?