For each 10,000-SNP reference panel, we imputed the 1,000 GWAS individuals using IMPUTE v2.1.2 and Beagle v3.0.2. We used the default settings for both methods (for IMPUTE2, the default khap setting is 500), and we also ran IMPUTE2 with khap set to include all available reference haplotypes. We recorded the single-processor running times and memory requirements for each run.
