Genotype level data from all studies were pre-phased with SHAPEIT2 (Delaneau, Zagury, and Marchini 2013), and imputed to the 1000 Genomes Project reference panel (Phase I integrated variant set release; NCBI build 37 (hg19)) using IMPUTE2 (Howie, Marchini, and Stephens 2011), using the Ricopili pipeline (Schizophrenia Working Group of the Psychiatric Genomics Consortium 2014). Prior to imputation, SNPs with call rate<0.98, minor allele frequency (MAF)<0.01, case-control differential missingness>0.02, Hardy–Weinberg equilibrium (HWE) p-values <1e-6 for controls and <1e-10 for cases were removed using PLINK (Purcell et al. 2007). After imputation, any SNPs with IMPUTE2 info score <0.6 and certainty <0.8 were removed. After splitting the datasets by sex, SNPs with MAF <0.05 were removed from each sex, because the number of subjects carrying the minor allele was too small and could give rise to false positive association results.
