Quality control of iPSYCH data mirrored the process implemented in the Psychiatric Genomics Consortium, with minor deviations in thresholds for exclusion (appendix p 9).3 As for deCODE, samples were assayed with several Illumina arrays at deCODE genetics. SNPs with low call rate (<95%), significant deviation from Hardy-Weinberg equilibrium (p<0·001), and excessive inheritance error rates (>0·001) were excluded. We did variant imputation on the basis of the IMPUTE HMM model and long-range phasing.19 Variants were further filtered for imputation INFO score more than 0·8 and minor allele frequency at least 1% before inclusion in meta-analysis.
