I am looking out to find out Unique SNP sharing between populations means common SNPs between a set of populations. I have merged set of VCF containing all population. What will be the possible workaround for this ? Each populations have several individuals. for exam we have Chinese population which consists of 5 samples VCF and then merge it into single VCF files which I call as population VCF. similarly we have for other's population too. I am thinking of using VCF tools (VCF-isec) to find the matching shared SNP between populations.
Can you guys suggest any other possible way apart from this also ? I mean can we get something from "FORMAT" section of VCF based on presence of population info ?