I have 3 vcfs with single sample each and different variants. I want one vcf with 3 samples and only variants that are present in all 3 vcfs.
I think I can do this a long way with
bcftools isec --nfiles 3 a.vcf b.vcf c.vcf
then grep out the list of variants present in all 3, do a filter step followed by standard
Is there any way to do this all in one step though?