or using only a smaller number of iterations (10–20) to estimate model parameters and then calculating maximum likelihood estimates for the missing genotypes and allele counts. Different chromosomes were analyzed in parallel and, overall, imputing genotypes for 2,335 unrelated individuals took <2 days for each of the largest chromosomes on a 2006 vintage 2.40GHz Pentium Xeon processor. In total, we imputed genotypes for 2,266,562 SNPs per individual. On average, our method used stretches of ~150 kb from the HapMap CEU panel to reconstruct haplotypes for individuals in the FUSION sample.
