python tools for aligning and translating subsequences containing SNPs

Question

[vdjonsson]

I am trying to develop a pipeline that will align a large number of subsequences of a certain length surrounding SNPs to the human genome, and then translate those subsequences to amino acid representations. I figure this should be straightforward using biopython and/or standard tools. However, I am not sure what the best way to do this is, and was wondering if I could get some insight into some of people's favorite tools.

Answer 1

[WouterDeCoster]

I'm not sure why you would like to do this in python. You probably need an aligner, a variant caller, and a tool like VEP or SnpEff to annotate these variants.

[vdjonsson]

Thanks for your comment, I'm just really looking for the best tools. I already have the location of the SNP, I just need to extract a surrounding subsequence, align it and translate it. I will look into the tools you mention, thanks!