An additional benefit of our method is that we can attempt to infer recombination events in trios and duos. Methods that explicitly phase trios and duos using the pedigree information cannot infer recombination events since they infer only the transmitted haplotypes of the parents. We evaluated this approach via simulation and found that we have power to detect events at a 5% false discovery rate when the duo is phased in an isolated cohort that may contain close relatives. When close relatives are removed we have power to detect events at a 5% false discovery rate. Cohorts that contain explicit trios and duos could be phased using methods that explicitly use this information if desired although the ability to infer recombination events would be lost and parents would be estimated as a pair of transmitted and untransmitted haplotypes.
