Use vcf files for dN/dS calculations
0
1
Entering edit mode
6.2 years ago
L. A. Liggett ▴ 120

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?

sequencing • 2.2k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2337 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6