On the full Scenario B dataset, we ran BEAGLE and IMPUTE v2 using the faster settings described above: 10 iterations for BEAGLE and k = 40 for IMPUTE v2. For each SNP that was not typed in the study sample, IMPUTE v2 used all observed reference panel chromosomes in each imputation step (1,956 states at SNPs in U2 and 120 states at SNPs in U1).
