Running times and memory requirements for various algorithms in Scenario B.

Running times are in minutes (min) and RAM requirements are in megabytes (MB). Each entry in the table is an average across eight runs, including four runs on different 7.5 Mb regions of chromosome 10 for study samples with either Affymetrix-only or Illumina-only SNPs masked. Each analysis included a haploid reference panel of 120 chromosomes (CEU HapMap), a diploid reference panel of 1836 chromosomes, and a study sample of 459 individuals. Numbers in parentheses represent analyses that included all SNPs that are polymorphic in the HapMap CEU panel; for the rest of the analyses, only SNPs that were genotyped on either the Affymetrix 500 K or Illumina 550 K chip were included in the HapMap dataset.*Unlike the other methods, IMPUTE v1 was not provided with the diploid reference panel. Consequently, these numbers are based on using a reference panel of 120 chromosomes to impute a study sample of 459 individuals.