Association analysis was done using logistic regression and the imputed marker dosages. The following covariates were used: principal component 1-4 and principal components from the PCA associated with case-control status, the 19 data-processing waves and diagnosis of major psychiatric disorders studied by iPSYCH (Supplementary Table 1). Results for 9,729,295 markers were generated, subsequently markers with imputation info score <0.7 (n=608.367), markers with maf <0.01 (n=10.220) and multi-allelic markers (n=143,083) were removed. In total after filtering 8,969,939 markers remained for further analysis. All analyses of the iPSYCH sample were performed at the secured national GenomeDK high performance-computing cluster in Denmark (https://genome.au.dk).
