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WHAP: haplotype-based association analysis.

Shaun Purcell·Mark J Daly·Pak C Sham
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Abstract

UNLABELLED: We describe a software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. A range of tests is offered: omnibus and haplotype-specific tests; prospective and retrospective likelihoods; covariates and moderators; sliding window analyses; permutation P-values. We focus on the ability to flexibly impose constraints on haplotype effects, which allows for a range of conditional haplotype-based likelihood ratio tests: for example, whether an allele has an effect independent of its haplotypic background, or whether a single variant can explain the overall association at a locus. We illustrate using these tests to dissect a multi-locus association. AVAILABILITY: WHAP is a C/C++ program, freely available from the author's website: http://pngu.mgh.harvard.edu/purcell/whap/

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AlgorithmsBase SequenceChromosome MappingGenetic MarkersGenetic VariationGenetics, PopulationHaplotypesLinkage DisequilibriumMolecular Sequence DataPolymorphism, Single NucleotideQuantitative Trait LociSequence AlignmentSequence Analysis, DNASoftwareStatistics as TopicJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't

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Shaun Purcell, Mark J Daly, Pak C Sham. 2006-11-21. WHAP: haplotype-based association analysis.. https://doi.org/10.1093/bioinformatics%2Fbtl580

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