hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups
Identification of recombination events and which chromosomal segments contributed to an individual is useful for a number of applications in genomic analyses including haplotyping, imputation, signatures of selection, and improved estimates of relationship and probability of identity by descent. Genotypic data on half-sib family groups are widely available in livestock genomics. This structure makes it possible to identify recombination events accurately even with only a few individuals and it lends itself well to a range of applications such as parentage assignment and pedigree verification.
phasing pedigree reconstruction recombination imputation haplotypes genotyping snp linkage analysis parentage testing