African LD files for GhostKnockoffGWAS

This contains pre-processed LD files (Sigma matrix, S matrix, ...etc) computed on African samples of the UK-Biobank (n = 5951). It is intended to be used as an input to the GhostKnockoffGWAS pipeline. 

This is the output of applying solveblock executable directly on 3394 African samples of the UK-Biobank.

Quasi-independent blocks are computed by applying the snp_ldsplit function with parameters thr_r2=0.01, max_r2=0.3, min_size = 500, and max_size = {1000, 1500, 3000, 6000, 10000}. 

SNPs with minor allele frequency less than 0.01 or Hardy-Weinburg equilibrium p-value less than 1e-6 are removed. 

Only HG19 coordinates are available. 

Knockoff optimization were carried out by the Knockoffs.jl julia package: https://github.com/biona001/Knockoffs.jl

The result (i.e. files available in this site) is saved in .csv and .h5 formatted files for easier access, which is directly readable by GhostKnockoffGWAS.