The existing summary statistics used in the present analyses have previously gone through quality-control pipelines used for the specific consortia (e.g. PGC quality control pipeline including filtering to remove SNPs with imputation information value < 0.90 and MAF < 0.01; Sullivan, 2010). The analytic pipeline for the present analyses incorporates further filtering processes including removal of SNPs based on a minimum Neff and per-SNP sample variation (e.g. SNP filtering keeping variants within at least 80% of the total Neff) and variants that are either not SNPs or are strand-ambiguous.
