I have 3 vcf files from different samples and would like to get a file with an intersection of common SNPs found in all 3 samples.
I have used bcftools isec for 2 samples first, took the intersection (either 0002.vcf or 0003.vcf generated from this) and then did another bcftools isec with the 3rd sample. However, I realised that only the samples present only belonged to the last sample group.
Could anyone advise on a way where I could receive an intersection of common SNPs found in all 3 samples with all samples present in the file?
Thank you very much!