We first tested our proposed imputation framework on a chromosome 20 dataset from HapMap 3. This dataset includes hundreds of haplotypes from each of several locations around the world, making it a good qualitative model for future reference panels like those being generated by the 1000 Genomes Project. The HapMap 3 panels used in this study are described in Table 1; note that we combined the CHB and JPT panels for this analysis.
