SNPs (k = 40 and k = 80, in separate runs) and 120 conditioning states (i.e., the full HapMap CEU panel) used for all haploid updates. We ran IMPUTE v2 with 10 burn-in iterations followed by 20 additional iterations. The first 3 burn-in iterations used random conditioning states for phasing updates, and all subsequent iterations used informed conditioning states. We discuss the motivations for these settings in Text S1.
