Chunk #31 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Detecting recombination events
Once all the haplotypes have been corrected the duoHMM is re-run in order to infer recombination events. We do this by calculating the probability of a recombination event between markers. A transition between the parental haplotypes corresponds to either a SE or a genuine recombination. A recombination event can only be resolved down to the region between its two flanking heterozygous markers in the parent. We use to be the indicator variable of a recombination event between heterozygous markers and . We evaluate the posterior probability of such a recombination event aswhereThe first and last probabilities can be calculated from the forward-backward algorithm, and the transition rates that include a recombination event are as followsNote since the loci between and are homozygous the emission probability is the same regardless of state, hence we do not require this term in the calculation. A recombination event is inferred whenfor some threshold . In the analysis in this paper we have used . To calculate these probabilities we tried using SHAPEIT2's most likely (pedigree corrected) haplotypes, or sampling haplotypes from SHAPEIT2's diploid graph
