We accommodate genotyping error by allowing for errors in the emission part of the HMM. We model the observed haplotypes at the th locus conditional upon the inheritance state as followsOur full model can then be written down asThis method can be applied to any set of estimated haplotypes from parent-child pairs. We run one iteration of the Forward-Backward algorithm [36] to estimate , and . Since there is little uncertainty in the state path this was found to be adequate for convergence. This estimation is carried out on each duo separately. Since the HMM has just four states the computation involved is negligible.
