SHAPEIT2, Beagle and HAPI-UR all provide functionality to phase parent-child duos and mother-father-child trios, by constraining the possible haplotypes to those consistent with the transmitted and untransmitted haplotypes of each parent (the child having each of the parents' transmitted haplotypes). This approach will produce very accurate haplotypes although will return the recombined haplotypes for each parent, rather than the true parental haplotypes. Since only several recombinations occur per chromosome, this is not introducing a substantial amount of error in the context of pre-phasing/imputation but is obviously problematic for researchers wishing to study recombination.
