Chunk #25 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Duo HMM

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A general approach for haplotype phasing across the full spectrum of relatedness.

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The initial states of the Markov model are given by . The transition rates on the IBD states are then given byThe sets denote the different types of transition that can occur. The set contains the transitions where no change in gene flow occurs. The set are the transitions with a change only to which of the parent's haplotypes are IBD. The set are the transitions with change only to which of the child's haplotypes are IBD. The set are the transitions with a change to both of child and parental IBD haplotypes. Figure 1 shows examples of how true recombination events and SEs in parental or child haplotypes lead to changes in the inheritance pattern in terms of , and events.