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 browse through the tutorial. Additional information is available in the documentation and download areas. The documentation is also available as a pdf file.

Broad Institute Users: You can install 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 it to run the program.

Credits

Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, Julian Maller, David Bender, and Jesse Whitworth. Questions and comments should be addressed to: haploview@broad.mit.edu

• 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.
• Hardy-Weinberg calculation code courtesy of Goncalo Abecasis and Jan Wigginton at the University of Michigan Center for Statistical Genetics
• 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.

Source Code

Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Citation

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.