For quality control of genotyped GWAS results, we removed SNPs that were only genotyped on our “V1” and/or “V2” platforms due to small sample size, and SNPs on chrM or chrY because many of these are not genotyped reliably. Using trio data, we flagged SNPs that failed a test for parent-offspring transmission; specifically, we regressed the child’s allele count against the mean parental allele count and flagged SNPs with fitted β<0.6 and P<10−20 for a test of β<1. We removed SNPs with a Hardy-Weinberg P<10−20 in Europeans; or a call rate of <90%. We also tested genotyped SNPs for genotype date effects, and removed SNPs with P<10−50 by ANOVA of SNP genotypes against a factor dividing genotyping date into 20 roughly equal-sized buckets. For imputed GWAS results, we removed SNPs with average r2<0.5 or minimum r2<0.3 in any imputation batch, as well as SNPs that had strong evidence of an imputation batch effect. The batch effect test is an F test from an ANOVA of the SNP dosages against a factor representing imputation batch; we removed results with P<10−50. Prior
