In preparation for imputation, we split phased chromosomes into segments of no more than 10,000 genotyped SNPs, with overlaps of 200 SNPs. We excluded SNPs with Hardy-Weinberg equilibrium P<10−20, call rate < 95%, or with large allele frequency discrepancies compared to European 1000 Genomes reference data. Frequency discrepancies were identified by computing a 2×2 table of allele counts for European 1000 Genomes samples and 2000 randomly sampled 23andMe customers with European ancestry, and identifying SNPs with a chi squared P<10−15. We imputed each phased segment against all-ethnicity 1000 Genomes haplotypes (excluding monomorphic and singleton sites) using Minimac231, using 5 rounds and 200 states for parameter estimation.
