I used three populations to call snps by SAMtools.And filtered biallelic snps by vcftools, I need to calculate between populations's fst, the original vcf file was divided into 3 sub-vcf files, each sub-vcf only contains two populations. The variant sites exist in the original vcf for three populations may not exist in the sub-vcf for two populations, because when extract only two populations, some sites should be the same between the included two populations but different from the third population, they are variants in the original vcf, but not variant any more in the sub-vcf. So, my question is how to delete these non-variant sites in the sub-vcf file? These sites genotypes are the same homozygote 0/0 or 1/1.
Is there any scripts or some softwares could address this?