Genotyping of the iPSYCH2012 sample was performed at the Broad Institute of Harvard and MIT (Cambridge, MA, USA) with PsychChip arrays from Illumina according to the manufacturer’s instructions. Genotype calling of markers with MAF≥0.01 was performed by merging call sets from GenCall 1.6.2.2101 and Birdseed 1.6102, and less frequent variants (MAF<0.01) were called with zCall 1103. Genotyping and data processing were carried out in 23 waves. Genotyping of the iPSYCH2015i sample was performed at Statens Serum Institut (SSI, Copenhagen, Denmark) using the Global Screening Array v2 with a multi disease drop in (Illumina, San Diego, California) according to the manufacturer’s instructions. Genotype calling of markers was performed using GenTrain V3. Preimputation quality control was performed separately for each genotyping wave using the Ricopili104 pipeline with the specified parameters in the following order. Initially SNPs with a call rate<0.95 were removed, and subsequently all individuals with a call rate in cases or controls of<0.95 or an autosomal heterozygosity deviation FHET outside the interval [−0.2;0.2] were removed. Individuals where stated sex was not consistent with sex derived from genotypes were flagged. Subsequently
