Extracting Codons from a SNP alignment

Question

[tpaisie]

Hi everyone,

So I have extracted SNPs from multiple different BAM files using Freebayes, filtered, and then used SnpEff to annotate my VCF file. So I have my SNP alignment in FASTA format, but I need to extract the codons from those SNPs. I realize SnpEff tells you were everything is, what its function is, but does anyone know a program that will take that information and actually give me the codons themselves? I feel like doing it manually is a lot of tedious work and would take a lot of time, and let's be honestly, no one has time for that. If there is a programming solution someone could suggest that would be great too. Python is my preferred language, but I would be happy to hear about any solutions that can be done in R. Any help would be greatly appreciated!!

[Joe]

You want the codon specifically that the SNP is a part of? Or you want to know what amino acid substitution (if any) has occurred because of it?

[tpaisie]

So the SnpEff annotation tells me the amino acid substitution and whether its in a coding or non-coding region. I need the codon for that specific SNP.

Answer 1

[rbagnall]

The web-based too SIFT/Provean will do this for you.

Given a list of input variants in the form of: chromosome,position,reference allele,alternate allele:

1,100382265,C,G

it will return: TCC [C/G]GA CAT (amongst other things) where your variant codon is in the middle and the flanking codons are either side.