Use vcf files for dN/dS calculations

Question

[L. A. Liggett]

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?

[rohitsatyam102]

Hi

Did you find a way to do this with a VCF file. I am also interested in calculating per-gene dN/dS ratio. I have multi-sample subset of the VCF file for each gene.

[wetdogsmell]

Have you already looked at dndscv? It might do what you are looking for.

[rohitsatyam102]

I want to try that but it asks for a Genomic Start and Coding Start and End Coordinates. Now since I have only GTF/GFF file for my organism from a source other than ENSEMBL I am finding it hard to understand how can I get Coding Start and End Coordinates.