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Chunk #48 — Online Methods — Genotype Data Processing and Imputation

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Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder.
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NSWBTRC samples were genotyped using the UK Biobank Axiom® Array (ThermoFisher Scientific, Waltham, MA, U.S.A.). Before imputation, palindromic SNPs and SNPs with genotyping rate <95%, minor allele frequency (MAF) <1%, or Hardy-Weinberg equilibrium P-value < 1E-4 were excluded. Genotype data was imputed by using the TOPMed Imputation Server.90 Eagle v291 was used to phase the genotypes and Minimac4 v1.2.490 was used for imputation. Data from the Trans-Omics for Precision Medicine (TOPMed r3)92 was used as the reference genomes.