Chapter 4. About Haploview

Haploview was developed in and is maintained by Mark Daly's lab at the Whitehead Institute by Jeffrey Barrett and Julian Maller.

  • The design of the interfaces is the work of Ben Fry at the MIT Media Lab.
  • Thanks to Andrew Kirby for large chunks of coding.
  • 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.

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]

Questions, complaints and suggestion should be directed to Jeffrey Barrett.

System Requirements

It is recommended that Haploview be run on a machine with at least 128M of memory. The Haploview jarfile should now automatically allocate extra memory when starting up, so the -Xmx flag is no longer required when running the program from the command line.

Haploview requires Java JRE 1.3 or later, but 1.4 is strongly recommended. It is worthwhile in any case to download the most recent Java release.

Known Issues

Saving PNG files from the command line (the -png and -compressedpng flags) requires Java version 1.4 or later.

There appears to be an issue with the Windows JDK version 1.4.1_03. Note that all other versions (both earlier and later versions of 1.4.1 included) seem to work fine. If you find this to be your current Java version (type java -version at the command prompt), please install the latest version.

Windows JDK version 1.3.1_02 seems to have trouble saving PNGs properly. Marker names are partially truncated in the saved file. Again, installing the latest version of Java should fix this issue.

Updates

If you have an internet connection, Haploview will automatically check for an update upon startup. If a new version is available, it will show a message in the lower right corner of the screen for a few seconds. Details can be found by using the "Check for Updates" button in the File menu.

Change Log

Version 3.11, 04 February 2005

  • improved parsing of families with unrelated members
  • fixed bug with singletons with large amounts of missing data
  • fixed bug with java path differences from cmd line
  • fixed export issues for LD display
  • fixed bug with block output for files without blocks

Version 3.1, 27 January 2005

  • Additional HapMap info track display options.
  • Improved parsing of complex pedigrees.
  • Fixed bug with loading of haps style input files.
  • Fixed bug with correctly parsing out-of-order info files.
  • Fixed problem with association tests on datasets with no blocks.
  • Fixed bug with exporting range of markers to LD PNG.

Version 3.0, 7 October 2004

  • bugfixes for block size display, checkdata tab, allele sorting, EM missing data.
  • Added compressed PNG output mode.
  • Lots of new command line options.
  • Changed batch mode input format.
  • Re-sort out of order info files.
  • Substantial improvement in speed and memory usage in EM.
  • New color schemes.
  • Added additional sample information for 2nd and 3rd HapMap plate.
  • Fixed handling of complex pedigrees.
  • Added proportional spacing to LD display.
  • Added HapMap GBrowse track.
  • Filter individuals with lots of missing genotypes.
  • Haplotype association tests.
  • Update checker.

Version 2.05, 27 April 2004

  • Fixed problem with EM for long blocks
  • Added "Export options" to allow exporting subsets of data and LD values for only adjacent marker pairs.
  • Numerous minor bugfixes
  • Added block labels to haplotype display
  • Added block size to LD display
  • Added saved block definition input file
  • Added analysis track input option
  • Enabled direct click from HapMap webpage to Haploview

Version 2.04, 21 January 2004

  • All color schemes now allowed with all block definitions, including hand-defined blocks.
  • Enabled loading input file from command line while still opening GUI.
  • Added command line HapMap Project input option.
  • Added colored box haplotype display.
  • Tweaked command line flags.
  • Added command line checkdata only output.
  • More accurate Hardy-Weinberg code implemented (courtesy of G. Abecasis & J. Wigginton).
  • Correctly deals with genotype inputs with poorly genotyped markers.

Version 2.03, 18 December 2003

  • Correctly handles new HapMap Project dump format.
  • Added minor allele frequency filter to data check tab.

Version 2.02, 05 December 2003

  • fixed confidence bounds coloring scheme bug
  • fixed text output bug where marker numbers were incorrect
  • added marker spacing map to top of HapMap datasets
  • added T-int statistic to text dump of LD chart

Version 2.01, 31 October 2003

  • fixed bug involving European style decimal format (e.g. 0,45 vs. 0.45)
  • when exporting data, default file name is now blank
  • marker info file now works in either forward or reverse direction
  • activated loading of HapMap Project dumped data