In the sections that follow, we describe the details of our new method as applied to the scenarios in Figure 1 and Figure 2. We then compare the method with other imputation approaches on real datasets from the United Kingdom that emulate Scenarios A and B. We show that our method can attain higher accuracy than existing methods in Scenario A, but that the absolute gains are small, which we attribute to the inherent limitations of a small set of reference haplotypes. In an example of Scenario B, we demonstrate that our method can use a large unphased reference panel to achieve higher accuracy than imputation based on the HapMap alone. We also show that our method can impute genotypes more accurately than other sophisticated [11],[13] and simpler [15] methods applied to the same dataset, and that our approach has higher sensitivity and specificity to detect copies of the minor allele at rare SNPs. In addition, we present results that highlight important practical advantages of our imputation modeling strategy over the one used by BEAGLE.
