We did a whole genome sequence of our samples and now we have a list of about 20,000 SNPs annotated against refgene (from UCSC). The list includes :
. chromosome . position of the SNP . within gene --> if yes, name of the gene . within CDS --> if yes, name of the gene . number of reads aligned against the SNP . number of reads aligned against the WT (refgene as a reference)
==> This list can be exported in a text file format.
From this, I need to extract Synonymous and Non Synonymous SNP.. I'm not in bio-informatic and know pretty know nothing about coding/developing- so I'm looking for a good tool that can do the job (if it does exist..). Our IT dept. went on vacation and unfortunately I'm left alone with this to do.
Any suggestion is always welcome~