WHAP: haplotype-based association analysis.
paper
Cited
Public
Unavailable
- Authors
- Purcell, Shaun; Daly, Mark J; Sham, Pak C
- Year
- 2007
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 17118959
- DOI
- 10.1093/bioinformatics/btl580
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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