Pre‐meta‐analysis QC were performed using EasyQC (Winkler et al., 2014). We filtered on sample MAF (0.03 for the largest dataset, MTFS; 0.04 for the intermediate datasets, COGA case control and QIMR BATS; and 0.05 for NTR and COGA EA), as well as EUR 1000 Genomes reference set MAF < 0.03, N < 200, HWE p < 10−7, INFO < 0.8, INFO > 1.05, imputation R 2 < .4, invalid numbers (Inf, NA), 0.2 difference between sample and reference set allele frequencies. Further checks consisted of matching alleles, duplicates, and strand flips. Meta‐analyzed SNPs were filtered for combined N > 6,000. The final datasets consisted of 4959085 to 4959521 SNPs depending on phenotype. Supporting Information Table shows the number of SNPs lost at each QC step for Cz alpha. Genome‐wide significance was set at 5 × 10−8.
