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Evaluation of the BEAGLE Haplotype Reconstruction Algorithm

Wednesday, August 20, 2014
Posters (The Westin Bayshore)
Mohammad Hossein Ferdosi , School of Environmental and Rural Science, University of New England, Armidale, Australia
Julius van der Werf , University of New England, Armidale, Australia
Bruce Tier , Animal Genetics and Breeding Unit, Armidale, Australia
Cedric Gondro , School of Environmental & Rural Science, University of New England, Armidale, Australia
Abstract Text:

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.

Keywords:

Haplotype reconstruction
Accuracy
Beagle

See more of: Posters: Methods and Tools - Bioinformatics
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