title: hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Here we present hsphase, an R package that exploits the genetic structure found in half-sib livestock data to identify and count recombination events, impute and phase un-genotyped sires and phase its offspring. The package also allows reconstruction of family groups (pedigree inference), identification of pedigree errors and parentage assignment. Additional functions in the package allow identification of genomic mapping errors, imputation of paternal high density genotypes from low density genotypes, evaluation of phasing results either from hsphase or from other phasing programs. Various diagnostic plotting functions permit rapid visual inspection of results and evaluation of datasets.
  
  
  CONCLUSIONS
  The hsphase package provides a suite of functions for analysis and visualization of genomic structures in half-sib family groups implemented in the widely used R programming environment. Low level functions were implemented in C++ and parallelized to improve performance. hsphase was primarily designed for use with high density SNP array data but it is fast enough to run directly on sequence data once they become more widely available. The package is available (GPL 3) from the Comprehensive R Archive Network (CRAN) or from http://www-personal.une.edu.au/~cgondro2/hsphase.htm.
authors.affiliation: The Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia. mferdosi@myune.edu.au.
authors.forename: Mohammad H
authors.initials: MH
authors.lastname: Ferdosi
authors.forename: Brian P
authors.initials: BP
authors.lastname: Kinghorn
authors.forename: Julius H J
authors.initials: JH
authors.lastname: van der Werf
authors.forename: Seung Hwan
authors.initials: SH
authors.lastname: Lee
authors.forename: Cedric
authors.initials: C
authors.lastname: Gondro
mesh_terms: D000818:Animals; D002417:Cattle; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006239:Haplotypes; D006720:Homozygote; D006801:Humans; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012756:Sheep
chemical_list: D005819:Genetic Markers