Formatted Public GWAS Summary Statistics for 16 Traits and LD pruned SNP sets

This data set includes 16 files with formatted GWAS summary statistic and a csv file gwas_info.csv. The csv provides the original download link and publication for each study. The data in this repository were created by downloading raw summary statistics for each study and processing them using Joe Marcus' GWAS pipeline (https://github.com/jhmarcus/gwass). The resulting data set have consistent allele orientation and column headers making them convenient for analysis. We use them in an MR analysis of pairs of GWAS traits described in Section 2.3 of  Morrison et al (2019) (https://www.biorxiv.org/content/10.1101/682237v3) and here https://jean997.github.io/cause/gwas_pairs.html.

New Sep 2022: I have added LD pruned SNP sets for each pair of traits.For each exposure/outcome pair, the set of snps in

snps_<exposure>__<outcome>.txt

were generated by LD pruning using LD estimated using LD Shrink (available https://zenodo.org/record/1464357/) at a threshold of r^2 < 0.1. LD pruning was performed using the ld_prune function in the cause R package (github.com/jean997/cause). These are the SNP sets used in the analysis in the paper