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A rapid conditional enumeration haplotyping method in pedigrees
Genetics Selection Evolution volume 40, Article number: 25 (2008)
Abstract
Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of the conditional probability of a haplotype configuration to the largest conditional probability of all haplotype configurations in order to eliminate those configurations with relatively low conditional probabilities. The new algorithm is much more efficient than our previous method and the widely used software SimWalk2.
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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Gao, G., Hoeschele, I. A rapid conditional enumeration haplotyping method in pedigrees. Genet Sel Evol 40, 25 (2008). https://doi.org/10.1186/1297-9686-40-1-25
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DOI: https://doi.org/10.1186/1297-9686-40-1-25