For each diploid proband in turn, Eagle analyzes overlapping ≈1cM windows of genome, searching for pairs of haplotypes (from the output of step 1) that approximately sum to the diploid proband within the window. Eagle then makes phase calls according to the haplotype pairs that most closely match the proband. In our N≈150,000 analyses, this step required ≈20% of the total computation time (Supplementary Table 2) and reduced the switch error rate to ≈1.5% (Fig. 1b). In more detail, our algorithm applies the following three procedures to each proband in turn.
