Chunk #27 — 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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We applied the duo HMM to the Beagle and SHAPEIT2 haplotypes from each cohort and examined the Viterbi paths for each duo. The Viterbi path is the most likely underlying state sequence, given the observed data [36]. We split duos according to the sex of the parent as we know that the rate of recombination events is higher in females than in males [37].