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A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

Figure 1

Examples of inferred haplotypes with true recombination events and SEs.

In each examples , , and denotes the two parental and child haplotypes and denotes the pattern of gene flow. Top: Correctly inferred haplotypes in a region of a true recombination event that causes a transition in the duo HMM. The other 4 examples in the figure add SEs to these true parental and child haplotypes. Middle left: addition of a SE in the child's haplotypes that causes a transition. Middle right: addition of a SE in the parent's haplotypes that causes a transition. Bottom left: addition of a SE in the parent's haplotypes at the site of the recombination event that causes the transition to be missed. Bottom right: addition of a SE in both the child's and parent's haplotypes at the same position that causes a transition.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1004234.g001