Chunk #29 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Correcting haplotypes
the or transitions is present in the same location for the majority of siblings, this is most likely a SE on the parental haplotypes and they can be corrected accordingly (see Figure S5 for an example of this process). This is not strictly the maximum-likelihood solution, but the minimum-recombinant and maximum likelihood solutions often yield the same result [38]. When we infer a SE in either a parent or a child we correct the haplotypes by switching the haplotype phase of all loci proceeding the SE. This procedure is carried out left to right along the sequence.
