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Chunk #12 — Materials and methods — Imputation and quality control — GS:SFHS

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Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank.
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52 monozygotic twin pairs, identified by IBD (preferentially retaining cases), and 7 individuals who matched samples from the Psychiatric Genomics Consortium, identified using genotype checksums24. After imputation, individuals with missingness ≥ 2%, and genotype with a call rate of ≤98%, MAF ≤ 0.5% and HWE P-value ≤ 1E-05 were excluded using PLINK version 1.9.25,26. Strand ambiguous SNPs with 40% ≤ MAF ≤ 50% were also excluded.