For the Psychiatric Genomics Consortium, standard procedures for GWAS quality control and imputation were applied using the Ricopili13 pipeline for case-control groups and the Picopili pipeline for family-based samples. Briefly, variants in each group were filtered for call rate (<5% missingness), followed by individual-level filtering for call rate (<2% missingness) and heterozygosity (|Fhet| <0·20). If available, chromosome X variants were checked to ensure concordance between genotype sex and reported sex. Variants were then filtered more stringently: variants with more than 2% missingness, differential missingness between cases and controls greater than 2%, invariant markers, and those departing from Hardy-Weinberg equilibrium in cases (p<1·00 × 10−10) or controls (p<1·00 × 10−6) were removed (appendix pp 8–10). Principal components analysis was done on a stringently quality-control set of variants using EIGENSOFT14, 15 to exclude population outliers, infer ancestry among the retained individuals (using the 1000 Genomes Phase 316 cosmopolitan reference panel), and derive ancestry-specific principal components for inclusion in analyses (appendix p 10). Sample and variant quality-controlled procedures, including filters for call rate, heterozygosity, and departure from Hardy-Weinberg equilibrium, were done within each
