For 52 cohorts internal to the PGC, genotyping was performed following local protocols and genotypes were called using standard genotype calling softwares from commercial sources (Affymetrix and Illumina). Subsequently, standardized quality control, imputation and statistical analyses were performed centrally using RICOPILI (Rapid Imputation for COnsortias PIpeLIne) (version 2018_Nov_23.001)94, separately for each cohort. Briefly, the quality control parameters for retaining SNPs and subjects were: 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, SNP Hardy-Weinberg equilibrium (P > 10 × 10−10 in psychiatric cases and P > 10 × 10−6 in controls). Relatedness was calculated across cohorts using identity by descent and one of each pair of related individuals (pi_hat > 0.2) was excluded. Principal components (PCs) were generated using genotyped SNPs in each cohort separately using EIGENSTRAT v6.1.495. Based on visual inspection of plots of PCs for each dataset (which were all of European descent according to self-report/clinical data), we excluded samples to obtain more
