I am trying to get my post GWAS data ready for pathway analysis. I have GWAS summary statistic files with SNPs(chr:pos) and p-values. I am looking for a tool that will map the SNPs to genes and give me an output file with gene names and corresponding p-values. What tools should I look at?
•
written
by
ssj.1503 •
I believe you first have to map snps to the gene (See VEP or BioMart) and than use vlookup to get corresponding p-values.
Thank you, but perhaps it's a bit more complicated? If multiple SNPs map to the same gene, I need a way to find the p-value for the gene. Some way to aggregate over all the SNP p-values?
You may want to try the VEP with the PostGAP plugin which calculates cumulative p-values on genes taking into account both overlap and known effects on gene expression.
You can use snpEff for variant annotation. Its is very easy to do it in SnpEff
Log in to answer this question.
There are many many posts already, please search for "snp to gene", "snp annotation", "positions to genes", etc