Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/14140
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)orcid ; Gondro, Cedric (author)orcid 
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
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Appears in Collections:Conference Publication
School of Environmental and Rural Science

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