I am trying to run a dN/dS calculation on some sequencing data of mine to understand positive and negative selection presence across different variants. Using my vcf files I was thinking of doing something like: samtools faidx ref chrom:low-high' to get a triplet context, and then make further calculations, but I do not know how to find the reading frame and codon in which a particular variant exists. Is there an easy way to get this?