The friendly GWAS SNP enrichment tool

User friendly program written in python and using bedtools to test for enrichment of GWAS SNPs in genomic annotation datasets. A specific feature is it tests for enrichment by locus not by individual SNPs. The user supplies 3 types of files. The first two files are a list of target SNPs and a list of background SNPs. To make the program user friendly the input format is simply the raw output from the popular haploreg program. Simply cut and paste that output into a text file. The genomic annotations are then supplied as bed files. The program will go through a directory of bed files e.g. all of the encode ChIP-seq datasets. Enrichment is checked against random samples from all the SNPs.
The output is a tab delimited text file with the number of target loci hit, the mean number of background loci hit, the fold enrichment and a P value derived from the number of background permutations that hit as many or more loci as the test SNPs, divided by the number of permutations.