Trait specific SNP prioritization
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5.1 years ago
LNA ▴ 30

Dear all, I am doing a GWAS for which I have only few samples available. According to the p-values I calculated using PLINK I don't have many significant signals. I would like to further investigate the SNPs with p-values in the "medium range" and now I am looking for a suitable prioritization tool, which can rank my SNPs according to the affiliation with keywords that are related to my studied trait (which could simply be a tissue type or more specifically proteins that are known to be important for the phenotype). A came across GeneSniffer, which seemed to use a list of keywords and a list of genes/SNPs to perform a ranking. Anyway, seemed to be doing what I would like to do, but it is not available anymore (or did I miss anything?).

Do you have any suggestions which tool would be best for this situation?

Thank you for your help!

SNP gwas enrichment prioritization • 1.2k views

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