Haploview

Formats

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Version 3.32, 21 June 2006

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  •  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

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  • fixed bug where chromosomes were created in reverse

Version 3.3, 26 May 2006

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  •  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

Version 3.2, 13 April 2005

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  •  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

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  •  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

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  •  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

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  •  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.

Version 2.05, 27 April 2004

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  •  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

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  •  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.
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