After initial sample and variant QC, principal components analysis (PCA) was used to identify population outliers for exclusion and to stratify samples in each study by continental ancestry. Identified EU and AA ancestry populations were confirmed by PCA using the 1000 Genomes reference panel21 (Supplementary Figure S12). Ancestry within these 2 groups was accounted for with principal components. Final sample and variant QC, including filters for call rate, heterozygosity, and departure from Hardy-Weinberg equilibrium (HWE), was then performed within each ancestry group in each cohort. Samples were also filtered for cryptic relatedness and for departures from reported pedigree structures (Supplementary Information A3; Life Sciences Reporting Summary).
