The standard PGC pipeline RICOPILI was used to perform QC, but modifications were made to allow for ancestrally diverse data. In the modified pipeline, each dataset was processed separately, including subjects of all ancestries. Sample exclusion criteria: using SNPs with call rates >95%, samples were excluded with call rates <98%, deviation from expected inbreeding coefficient (fhet < −0.2 or >0.2), or a sex discrepancy between reported and estimated sex based on inbreeding coefficients calculated from SNPs on X chromosomes. Marker exclusion criteria: SNPs were excluded for call rates <98%, a > 2% difference in missing genotypes between cases and controls, or being monomorphic. Hardy-Weinberg equilibrium (HWE): the modified pipeline identified the largest homogenous ancestry group in the data, identified SNPs with a HWE P-value < 1 × 10−6 in controls, and excluded these SNPs in all subjects of the specific datasets, irrespective of ancestry.
