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I have a list of all SNPs (a list of RsIDs) that fall in the coding sequence of several thousand human genes, and I'm looking for a convenient method to come up with a list of known SNPs that alter an amino acid in those genes.
I'll be glad to hear your thoughts.
What you are looking for is SNP annotation. If you have the chromosome:position reference and alternate alleles for your SNPs of interest, it can be as simple as uploading them to the variant effect predictor.
http://grch37.ensembl.org/Homo_sapiens/Tools/VEP
This will give you the predicted protein change and novelty of the variant with respect to known variation in large scale sequencing projects like the 1000 genomes.
If you cannot afford to upload data on the web, there are downloadable command line software like SNPeff, Variant effect predictor etc but it would require some more bioinformatics knowledge of converting your data to a VCF format and obtaining a human reference genome.
ANNOVAR is another tool that will help you functionally annotate genetic variants. It will tell you if the variant is known in COSMIC or Clinvar databases, which AA change will occur, if it's a frameshift, synonymous, non-synonymous, etc...
