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Bioinformatics. 2007 Jan 15;23(2):255-6. Epub 2006 Nov 21.

WHAP: haplotype-based association analysis.

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  • 1Center for Human Genetic Research, MGH, Boston, MA, USA.


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.


WHAP is a C/C++ program, freely available from the author's website:

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