Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently supports the following functionalities:
LD & haplotype block analysis
haplotype population frequency estimation
single SNP and haplotype association tests
permutation testing for association significance
implementation of Paul de Bakker's Tagger tag SNP selection algorithm.
automatic download of phased genotype data from HapMap
visualization and plotting of PLINK whole genome association results including advanced filtering options
Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals.
The best way to become familiar with Haploview is to get the software and go through the tutorial. Additional information is available on the documentation page.
Broad Institute Users: You may run the newest version of the program without administrator privileges on your computer by saving the Haploview.jar file to your local user folder and double clicking on it.
Questions and Help Requests
Haploview is currently on a development and support freeze and so there is no help provided. The team is currently looking at a variety of options in order to provide support for the software.
Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth.
The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab.
Thanks to Andrew Kirby and Hin-Tak Leung for code contributions.
Thanks to Itsik Pe'er and Paul de Bakker for their extensive contributions to methods development and testing.
The r2 and alternative D' color schemes are the work of Will Fitzhugh.
The interface to the HapMap GBrowse track is courtesy of Simon Twigger.
PLINK is the work of Shaun Purcell at the Center for Human Genetic Research of Massachusetts General Hospital.
GeneCruiser is the work of The GeneCruiser Team at the Broad Institute of MIT and Harvard.
Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.
Haploview can be cited with the following paper: Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005 Jan 15 [PubMed ID: 15297300]
Information about the exact test for HW can be found in the following paper: Wigginton JE, Cutler DJ, Abecasis GR. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet. 2005 May;76(5):887-93.
Information about parenTDT can be found in the following paper: Purcell S, Sham P, Daly MJ. Parental phenotypes in family-based association analysis. Am J Hum Genet. 2005 Feb;76(2):249-59.
For a general listing of papers that mention Haploview can be found HERE. This will link directly to Google Scholar.