European (British) LD files for GhostKnockoffGWAS

This contains pre-processed LD files (Sigma matrix, S matrix, ...etc) computed on unrelated British samples of the UK-Biobank (n = 306604). It is intended to be used as an input to the GhostKnockoffGWAS pipeline. 

This is the output of applying solveblock executable directly on 306,604 unrelated British 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. 

Note: We previously released another set of EUR LD files. This set of LD files should be preferred over the previous one. The main difference with this entry is that the previous entry used quasi-independent blocks from LDetect computed on the 1000 genomes project. Here we compute the independent blocks using snp_ldsplit directly on the UK-Biobank British samples.