A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
The four possible IBD states (A, B, C, D) are shown using colours pale blue, dark blue, light red and dark red respectively. The left and right panels show the results of the duo HMM applied to the SHAPEIT2 and Beagle haplotypes 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. The x-axis shows the sex-averaged genetic distance across the chromosome in centiMorgans.