European LD files for GhostKnockoffGWAS

DOI10.5281/zenodo.10433663Zenodo10433663MaRDI QIDQ6678944FDOQ6678944

Dataset published at Zenodo repository.

Benjamin B Chu

Publication date: 20 February 2024

Copyright license: Creative Commons Attribution 4.0 International

Description

This contains pre-processed LD files (Sigma matrix, S matrix, ...etc) computed on the EUR cohort of Pan-UKB LD data. It is intended to be used as an input to the GhostKnockoffGWAS pipeline. We restricted our attention to the EUR panel We filtered the original HailBlockMatrix LD panel to genotypes that are typed (i.e. imputed SNPs were removed) Coordinates in both hg19 and hg38 are available. Conversion from hg19 to hg38 were achieved by the R package liftOver. Downloading and processing of the original HailBlockMatrix formatted data is accomplished by the EasyLD.jl software: https://biona001.github.io/EasyLD.jl 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.

This page was built for dataset: European LD files for GhostKnockoffGWAS