mendeloverlap

README

Mendeloverlap

Mendel overlap helps assess the degree to which your GWAS loci overlap with a Mendelian gene list beyond what would be expected by chance. It requires that you provide a gene list (just a file with each gene name on its own line) and the output from SNPsnap. SNPsnap is a tool that takes in your GWAS SNPs and returns similar SNPs (in terms of allele frequency, gene density, etc) to make for a fair permutation. The tool then tests how many genes are within a radius from your real loci and your SNPsnap permutation loci, providing a P-value.

Once mendeloverlap is installed (go install), it can be run as follows:

mendeloverlap \
  -snpsnap snpsnap_output.txt \
  -radius 250 \
  -mendel cardiomyopathy_genes.csv

Run it without arguments to see the different toggles that are available.

Documentation

Overview

MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest. GRCh37 only.