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|Title:||Effect of genotype and pedigree error on detection of recombination events, sire imputation and haplotype inference using the HSPhase algorithm||Contributor(s):||Ferdosi, Mohammad (author); Kinghorn, Brian (author); Van Der Werf, Julius H (author) ; Gondro, Cedric (author)||Publication Date:||2013||Handle Link:||https://hdl.handle.net/1959.11/14140||Abstract:||HSPhase is a fast and accurate algorithm for detection of recombination events, sire imputation and haplotype inference of half-sib families. It can be used on data for half-sib families with as few as 4 individuals in a family. The robustness of this algorithm in relation to genotype and pedigree errors was evaluated. If there were more than 20 half-sibs in a family, the performance of the algorithm with 5% pedigree or genotyping errors was still reliable with the accuracy of phasing and imputation above 0.87. These error rates are above those commonly observed in industry data which indicates the algorithm is sufficiently robust for deployment in real world settings. An R package implementing the method is freely available and includes a function to generate diagnostic plots which are very useful to rapidly identify problems in the dataset.||Publication Type:||Conference Publication||Conference Name:||20th Conference of the Association for the Advancement of Animal Breeding and Genetics: Translating Science into Action, Napier, New Zealand, 20th - 23rd October, 2013||Conference Details:||20th Conference of the Association for the Advancement of Animal Breeding and Genetics: Translating Science into Action, Napier, New Zealand, 20th - 23rd October, 2013||Source of Publication:||Proceedings of the Twentieth Conference of the Association for the Advancement of Animal Breeding and Genetics, p. 546-549||Publisher:||AAABG: Association for the Advancement of Animal Breeding and Genetics||Place of Publication:||Palmerston North, New Zealand||Field of Research (FOR):||060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)||Peer Reviewed:||Yes||HERDC Category Description:||E1 Refereed Scholarly Conference Publication||Other Links:||http://www.aaabg.org/aaabghome/proceedings20.php||Series Name:||Proceedings of the AAABG ... Conference||Series Number :||20||Statistics to Oct 2018:||Visitors: 326
|Appears in Collections:||Conference Publication|
School of Environmental and Rural Science
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