The Beagle haplotypes contain many more , and transitions. In the Val Borbera cohort when we compared the SHAPEIT2 and Beagle haplotypes to those estimated by Merlin we found that SHAPEIT2 produced 4,613 SEs in 1,074 individuals corresponding to 4.3 switches per individual, whereas Beagle produced 29,681 switches or 27.6 switches per individual. These numbers seem consistent with what we observe in Figure 3. The higher rate of SEs in the Beagle haplotypes cause a large number of changes in estimated IBD state.
