Figure 3 shows a striking difference between the output on the SHAPEIT2 and Beagle haplotypes. The SHAPEIT2 paths have very few transitions of all types, and when transitions occur they are predominantly transitions. The figure shows only father-child duos and chromosome 10 has been estimated to have a genetic length of 1.34 Morgans for paternal meioses [37]. The numbers of transitions in the 50 duos in Figure 3 looks reasonably consistent with this genetic length, suggesting that the transitions are indeed true recombination events. We note that there are some duos with no transitions. This is a possible outcome of a meiosis and is more likely to occur on the shorter chromosomes, and can also be the product of undetected recombination events.
