Technical Quality control was performed on the core PGC cohorts separately according to standards developed by the PGC3 including SNP missingness < 0.05 (before sample removal); subject missingness < 0.02; autosomal heterozygosity deviation (| Fhet | < 0.2); SNP missingness < 0.02 (after sample removal); difference in SNP missingness between cases and controls < 0.02; and SNP Hardy-Weinberg equilibrium (HWE: P > 10−6 in controls or P > 10−10 in cases). For family-based cohorts we excluded individuals with more than 10,000 Mendelian errors and SNPs with more than 4 Mendelian errors. For X-Chromosomal genotypes we applied an additional round of the above QC to the male and female subgroups separately.
