leadSNP

Identify list of potential novel SNPs associated with disease. Requires 1) clumped GWAS output, 2) list of established loci (from literature), 3) plink LD out for all clumped SNPs (experimental + established)

R functions

clump.import, snp.block, snp.novel, ld.annotate, snp.annotate, snp.coordinates

Example on how to preformat the input files from using prep.sh

Nice to add: summary stats on how many regions, novel, established, etc..