Hi, I have a VCF containing the SNP information between the two genotypes of interest and using that VCF and i have annotated the SNPs using snpeff annotation tool. SNPeff does a good job annotating the SNPs in terms calculating the number of Non-Synonymous and Synonymous SNPs. One of the thing i am interested is the calculating the dN/dS ratio for each of the chromosome for the two genotypes. I did that, but some one recently told me that the before calculating dN/dS ratio, i should be estimating Non-Synonymous and Synonymous sites and then calculate dN/dS ratio. So i am wondering how do one go about estimating Non-Synonymous and Synonymous sites using VCF file?