Chunk #20 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error

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

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The results below show that SHAPEIT2 can implicitly leverage IBD sharing and hence phase a pedigree accurately without any relationships specified. Additional use of explicit relationships is likely to lead to even greater improvements. The Lander-Green algorithm is traditionally the method of choice for phasing pedigrees but has several limitations described previously. We developed a simple HMM applicable to the SHAPEIT2 haplotypes that corrects phasing errors that are inconsistent with pedigree information. The method focuses separately on each parent-child duo and this circumvents several issues with the Lander-Green algorithm, namely;