Table 2 also shows the haplotype accuracy for pedigrees that were partitioned into duos and trios and then phased accordingly using Beagle (denoted as Beagle Duo/Trio). Not surprisingly, adding the duo/trio relationships yields a substantial improvement to the Beagle haplotypes across all cohorts; for example we see a drop from 1.362% SE to 0.445% SE in CARL. However they are still consistently less accurate than SHAPEIT2's haplotypes (even though SHAPEIT2 is not using any relationships).
