Dear Biostars,
I am new at the GWAS-World and I search for a Tool which definitely should be some where but I do not find anything on Google.
I have a plink file (.bed, .bim, .fam to one Dataset). The data is already cleaned up and every Sample has a List of dbSNPs that contain the calls (shown in the Picture). I want to remove every row where the dbSNP is known as a synonym variant. In this case the variant produces the same amino acid and has probably no impact on the protein. So I want to remove every rsXXXXXXX that is labeled synonymous variant[Function_Class] on NCBI. Is there a tool which can automatically remove these rows and give me a shorten list?
The only thing that I find is PLINK which had the function lookup, but this is not supported anymore. PLINK/SEQ should replace it but there is no direct download file for installation.
Any thoughts on this?
