A big disadvantage of existing pedigree analysis software is the inability to leverage wider cohort information to resolve sites that are heterozygous throughout a particular pedigree. Hence there is a need for software that can fully leverage the relatedness within pedigrees for accurate phase whilst overcoming the limitations of traditional pedigree analysis software. We propose a two-stage approach in which SHAPEIT2 is first run ignoring all explicit family information. We then apply the duoHMM method to incorporate the pedigree information in a cohort to further increase the accuracy of haplotypes inferred. The duoHMM method infers the inheritance pattern in parent-child duos, detects genotyping errors and can correct switch errors.
