When using the Beagle Duo/Trio method some individuals will not be phased as part of a duo or trio, for example one of the children in a three sibling nuclear family. Figure 4 (top and centre left) plots the SE for such “unrelated” individuals for Beagle Duo/Trio versus SHAPEIT2 and Beagle Duo/Trio versus SHAPEIT2+duoHMM respectively. These plots show that these individuals are phased much more accurately using our methods. Duos and trios are phased almost equally well by all methods.
