LD Pruned GWAS SNP Set Readme New LD pruned subset to try for GWAS: As before, it is based on the Filtered SNP set (4.8M) which is a subset of Base SNP (18M), unlike the 990k SNP set. It was done with just one round of LD pruning, r2 cutoff 0.8, window size 2kb and step 1 SNP, so that we will remove only SNPs that are less than ~2kb apart. This leaves 1,011,601 snps.