samples with sex mismatch. Imputation was performed using Eagle v2.4 (for pre-phasing) [35] and Minimac4 [36] with 1KG phase 3 data as the reference panel. We randomly removed one sample from each related pair of individuals within or across batches, leaving 25,110, 54,078, and 10,378 individuals for the three batches, respectively (Table 1). Post-imputation QC excluded variants with imputation quality scores <0.6 and MAF <0.5%.
