We next used the McCarthy tool to match the SNPs to 1000 Genomes, and Genotype Harmonizer software (automatic strand alignment software) to align the different cohorts (25). After QC, we merged the cohorts based on the set of all intersecting SNPs and performed additional QC as noted in Supplementary Materials. The final data set included 2090 cases and 4567 controls, with 412,813 SNPs (Table 2).
