Post GWAS mapping SNPs to genes and calculating p-values

Question

[ssj.1503]

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?

[zx8754]

There are many many posts already, please search for "snp to gene", "snp annotation", "positions to genes", etc

• Map SNP names to gene symbol
• How To Map A Snp To A Gene Around +/- 60Kb ?
• SNP to gene mapping into reference genome
• Get gene names from rs SNP ids
• Mapping Snps To Pathways
• How to get gene name for SNPs RS ids

Answer 1

[tothepoint]

I believe you first have to map snps to the gene (See VEP or BioMart) and than use vlookup to get corresponding p-values.

[ssj.1503]

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?

[Emily]

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.

Answer 2

[biotechnology415]

You can use snpEff for variant annotation. Its is very easy to do it in SnpEff