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Title: Evaluation of the BEAGLE Haplotype Reconstruction Algorithm: Using Half Sib Families to Evaluate the Accuracy of Haplotype Reconstruction
Contributor(s): Ferdosi, M H  (author)orcid ; van der Werf, J H J  (author)orcid ; Tier, B  (author); Gondro, C  (author)orcid 
Publication Date: 2014
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Abstract: The BEAGLE program is frequently used for haplotype reconstruction using dense molecular marker genotype data in animal, plant or human populations. In this study, we evaluate the accuracy of BEAGLE for phasing with a population that consists of large half-sib families. The half-sib structure allows the accurate detection of phase thus making it easier to detect problems in more general population based algorithms such as BEAGLE. We show that the main problem in the haplotypes inferred by BEAGLE is the occurrence of switch errors where the parental origin of haplotypes is incorrectly swapped. This occurs especially in the large chromosomes and often in ~50% of individuals. Understanding the issue will allow better decision making about further analyses that relies on the haplotype origin of markers.
Publication Type: Conference Publication
Conference Details: WCGALP 2014: 10th World Congress on Genetics Applied to Livestock Production, Vancouver, Canada, 17th - 22nd August, 2014
Source of Publication: Proceedings of the 10th World Congress on Genetics Applied to Livestock Production (WCGALP) (Methods and Tools: Bioinformatics (Posters)), p. 1-3
Publisher: American Society of Animal Science
Place of Publication: Champaign, United States of America
Fields of Research (FoR) 2008: 070201 Animal Breeding
Fields of Research (FoR) 2020: 300305 Animal reproduction and breeding
Socio-Economic Objective (SEO) 2008: 830310 Sheep - Meat
830311 Sheep - Wool
Socio-Economic Objective (SEO) 2020: 100412 Sheep for meat
100413 Sheep for wool
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication
School of Environmental and Rural Science

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