Prior to imputation, Mendelian inconsistences were detected using Pedcheck (O’Connell and Weeks, 1998), and genotype inconsistences were set to missing. Variants with missing rates >5%, MAF <3% and HWE p values <0.0001 were excluded. In addition, variants with A/T or C/G alleles were also removed to avoid ambiguities in strand designation. SHAPEIT2 (Delaneau et al., 2013), which utilizes pedigree information to increase accuracy, was used to phase haplotypes of each sample. All samples were imputed to 1000 Genomes the cosmopolitan reference panel (Phase 3, version 5, http://www.internationalgenome.org/) using Minimac3 (Das et al., 2016). Due to the differences in the variants on each array, samples were imputed separately by array. After imputation, variants with R2 <0.30 were excluded. To allow for further Mendelian error checking, genotype probabilities were converted to genotypes if they were ≥0.90 (similar to procedures for QC and analysis of family data in Walters et al., 2018 (Walters et al., 2018); see also Kranzler et al., 2019 that used converted genotypes (Kranzler et al., 2019)). All genotype and imputed variants with missing rates <20%, MAF ≥1% and HWE
