We applied our duoHMM method to the SHAPEIT2, Beagle and HAPI-UR haplotypes that were estimated ignoring all family information. To give a sense of the output of applying this model Figure 3 shows the Viterbi paths of 50 male parent duos from the Val Borbera cohort for both SHAPEIT2 and Beagle. The four possible IBD states are shown using colours pale blue, dark blue, light red and dark red respectively. Changes between a blue and red colour correspond to a or transition, both of which imply a SE in the child. Changes of colour between light and dark blue or between light and dark red correspond to transitions, which correspond to a change on IBD state in the parent, and could be caused by a recombination or a SE in the parent. Figure 1 provides examples that can be helpful in interpreting Figure 3. Figures S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22 show the Viterbi paths of male parent and female parent duos for all of the cohorts.
