Now showing items 1-5 of 5

    • Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations 

      Ros Freixedes, Roger; Whalen, Andrew; Chen, Ching-Yi; Gorjanc, Gregor; Herring, William O.; Mileham, Alan J.; Hickey, John M. (BMC (part of Springer Nature), 2020-04-06)
      Background: The coupling of appropriate sequencing strategies and imputation methods is critical for assembling large whole-genome sequence datasets from livestock populations for research and breeding. In this paper, we ...
    • Assessment of the performance of hidden Markov models for imputation in animal breeding 

      Whalen, Andrew; Gorjanc, Gregor; Ros Freixedes, Roger; Hickey, John M. (BMC (part of Springer Nature), 2018-09-17)
      Background: In this paper, we review the performance of various hidden Markov model‐based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic‐based imputation methods have been used for ...
    • Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling 

      Ros Freixedes, Roger; Whalen, Andrew; Gorjanc, Gregor; Mileham, Alan J.; Hickey, John M. (BMC (part of Springer Nature), 2020-04-06)
      Background: For assembling large whole-genome sequence datasets for routine use in research and breeding, the sequencing strategy should be adapted to the methods that will be used later for variant discovery and imputation. ...
    • Genetic variation in recombination rate in the pig 

      Johnsson, Martin; Whalen, Andrew; Ros Freixedes, Roger; Gorjanc, Gregor; Chen, Ching-Yi; Herring, William O.; Koning, Dirk‑Jan de; Hickey, John M. (BMC (part of Springer Nature), 2021-06-25)
      Background: Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by ...
    • Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees 

      Whalen, Andrew; Ros Freixedes, Roger; Wilson, David L.; Gorjanc, Gregor; Hickey, John M. (BMC (part of Springer Nature), 2018-12-18)
      Background: In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, ...