Chunk #28 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Correcting haplotypes
We now describe how to use our model to adjust haplotypes so that they are consistent with a given pedigree structure. After estimating parameters, we run the Viterbi algorithm to find the most likely state sequence. There are sixteen possible state transitions in our model. The eight transitions in the sets and imply a SE in the child haplotypes, so when we observe one of these transitions in the Viterbi sequence we infer a SE in the child. The eight transitions in the sets and imply either a SE or a recombination event in the parental haplotypes. Inferring whether a recombination or a SE has occurred in the parental haplotypes is difficult. When more than one sibling is present in a pedigree, we can correct probable parental SEs via identifying the minimum recombinant haplotypes for the family. When one of 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
