hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups

• Published in: BMC bioinformatics Vol. 15; no. 1; p. 172
• Main Authors: Ferdosi, Mohammad H, Kinghorn, Brian P, van der Werf, Julius HJ, Lee, Seung Hwan, Gondro, Cedric
• Format: Journal Article
• Language: English
• Published: London BioMed Central 07.06.2014; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Animals; Bioinformatics; Biomedical and Life Sciences; Cattle; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Genetic Markers; Genetic structure; Genome; Genomics; Genomics - methods; Genotype; Genotypes; Haplotypes; Homozygote; Humans; Life Sciences; Livestock; Microarrays; Offspring; Pedigree; Polymorphism, Single Nucleotide; Recombination, Genetic; Sequence analysis (methods); Sheep; Software; Haplotypes; Recombination; SNP; Genotyping; Parentage testing; Imputation; Pedigree reconstruction; Phasing; Linkage analysis
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-15-172

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. Conclusion 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 .