Genotype data was processed separately by study. For genotype data processed by the PGC-PTSD analyst, quality control was performed using a uniform set of criteria, as implemented in the RICOPILI85 pipeline version 2019_Oct_15.001. Modifications were made to the pipeline to allow for ancestrally diverse data and are noted where applicable. Quality control: 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. SNPs were excluded for call rates <98%, a > 2% difference in missing genotypes between cases and controls, or being monomorphic. Hardy-Weinberg equilibrium was calculated within only in the largest homogenous ancestry group found in the data. SNPs with a Hardy-Weinberg equilibrium P-value < 1 × 10−6 in controls were excluded.
