Chapter 4. About Haploview
Haploview was developed in and is maintained by Mark Daly's lab
at the Broad Institute by
Jeffrey Barrett, Julian Maller and David Bender. 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 Media
Lab.
- 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
Source Code
Haploview is an open source project hosted by
SourceForge. The source can be downloaded at
the SourceForge project
site.
Citations
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.
Questions, complaints and suggestion should be directed to
haploview@broad.mit.edu.
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.
We are working to correct a rare issue with Spineblock outputs for
certain datasets.
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.
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.
Version 4.1, 29 April 2008
- added support for GeneCruiser lookup
- added support for HapMap release 22
- added -out fileroot specification to the command line
- added consecutive filtering to PLINK with view/add/remove filters
- added SVG output for LD plot and haplotype blocks display
- added min design scores to Tagger in GUI and command line
- added reset thresholds button to Tagger
- added exclude A/T and C/G SNPs button to Tagger
- upgraded graphing packages to latest version
- changed load screen dialog tab orientation for Mac OSX
- fixed bug with LD display pop-up on certain systems
- fixed bug with HapMap info track caching
- fixed bug on LD Display with MAF of .5
- fixed bug where setting tagger cutoff fields to blank would generate exceptions
- fixed bug with PLINK View Filters dialog
- fixed bug with PLINK file column number mismatches
Version 4.0, 21 August 2007
- added support for HapMap PHASE format data
- added support for phased HapMap downloads
- added support for PLINK output files including plotting functionality
- added a number of Tagger features to coincide with the Tagger website functionality
- added 2-marker aggressive tagging from the command line
- added log file functionality to command line mode
- added proxy support
- added table sorting to Tagger configuration
- added numerous minor display and interface tweaks
- added export options for Mendel errors and male heterozygotes on x chromosome
- added command line HapMap info track download
- added case control frequencies to command line association output
- added ld values selection to command line image export
- added citation information to the "About" dialog
- added "Uncapture All" button to Tagger
- added build 36 option to HapMap info track downloads
- added http:// loading for files on the command line and initial load screen
- changed some labelling in Tagger and made pairwise the default option
- changed obsHet calculation to use founders only
- changed HW and het calculations to show as "NA" in X data with too few individuals
- enhanced GUI design with tabbed pane for initial loading dialog
- fixed bug with haplotype associations for extended trios and x chromosome
- fixed bug with case control counts for certain zeroed out markers
- fixed Mendel error reporting bug on x chromosome
- fixed Tagger bug affecting maximum number of tags input
- fixed bug when left-clicking on the LD plot
- fixed bug when changing tabs after multiple file loads
- fixed bug when changing tabs after running tagger and changing check marker thresholds
- fixed bug when loading custom association test file with multi-marker tests but no alleles
- fixed bug with long windows filenames in command line mode
- fixed bug with display when resizing the window to a very small size
- fixed bug with 'h' alleles in haps files not being properly calculated
- fixed bug with check panel export not accounting for user threshold adjustments
- fixed bug with LD display where some r^2 values were invisible against the background
- fixed bug with integer overflow when loading files with tens of thousands of individuals
- fixed bug where HapMap info track would turn black if it was too wide
- fixed bug with null pointer exception on failed hapmap info track downloads
- fixed bug with null pointer exception when using Export Options Dialog
- fixed bug with LD Plot now showing the correct markers when changing marker ratings and using table sorting in the check panel
- fixed tagger results reporting of % captured when specifying alleles to capture
- fixed bug with marriage loops in pedigree files causing StackOverflow errors
- fixed bug with exception being thrown for certain input files with no markers
- fixed bug with multimarker tags showing in the tagger results even though they don't capture anything
- fixed bug with command line error handling
- fixed bug with loading improperly formatted info files from "Load marker data"
Version 3.32, 21 June 2006
- fixed bugs in check markers display when using table sorting
- fixed line number output on error messages
- grammar corrections
Version 3.31, 2 June 2006
- fixed bug where chromosomes were created in reverse
- support for X chromosome
- major memory usage improvements
- allow multiple analysis tracks and label Y axis
- added user defined hapmap sample option
- added haplotypes only permutation option
- added option to show different LD measures or hide them
- added -memory switch and changed default to 512M
- added minor allele to check panel
- added progress bar for data loading
- support for alphabetical (ACGT) input format
- added individual information dialog
- added check panel for phased haps files
- added dump tags button
- last popup dialog is shown at top of display
- added GOLD style color scheme
- can sort tables by clicking on headers
- changed case control allele order
- fixed grey screen with no text bug
- fixed tagger bugs for maxnumtags and forceinclude
- fixed batch mode for hapmap files
- fixed Tagger bug where some SNPs were tagged by more than one tag.
- fixed export options bug with association tab
- fixed generateHaplotyeps bug for matching alleles
Version 3.2, 13 April 2005
- added Tagger interface
- added custom association test input
- added permutation testing of association results
- improved memory efficiency for EM haplotype reconstruction
- added Perlegen sample IDs
- fixed bug in PNG export cutting off final marker
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