Figure S5 shows the results of applying our duo HMM on the SHAPEIT2 haplotypes of all father-child duos in a three sibling family before and after using our correction method. Before correction (Figure S5 (left)), the first father-child duo exhibits no evidence of recombination (change in colour between dark and light red) and these two individuals share a whole haplotype across the whole chromosome. The other father-child duos show evidence of 3 and 4 recombination events respectively, with one event being shared in common at . Our method infers a parental SE at this location. This has the effect (Figure S5 (right)) of reducing the total number of inferred recombination events across the 3 duos from 0, 3 and 4 to 1,2 and 3, which seems more realistic.
