I have a VCF with SNPs for several strains of mice. I would like to extract the nonsynonymous SNPs and create alternate peptide sequences for each strain. I can do this by hand with several lines of code, but I'm wondering if there is a pipeline or a package that can do this?  The functionality would be something like predictCoding(), but it would also insert the alternate amino acid into the protein sequence.

Thanks,

Daniel Gatti

The Jackson Laboratory