Chunk #30 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Correcting haplotypes
Corrections are applied sequentially ‘down’ through each pedigree. For example, in a three generation (grandparent-parent-child) pedigree we first apply the method to those duos containing grandparents. Any corrections made to the parents haplotypes are used when processing duos involving those parents and their children. This removes any (detectable) SEs for individuals that have parents, before their descendants are phased. We applied our method of correcting haplotypes to all of the chromosome 10 haplotypes produced by SHAPEIT2, Beagle and HAPI-UR in all cohorts and evaluated the improvements in accuracy as well as the number of corrections that were required.
