IGV 2.0.x

IGV 2.0.35 released January 14,  2012

  • Add support for indexed fastas in ".genome" files.

IGV 2.0.34 released January 14,  2012

  • Bug Fixes
    • Data in BigWig tracks could disappear when zoomed in if chromosome aliases were used.
    • Negative strand CDS features in GFF files not translated properly.
    • Dragging a track into an empty panel would cause it to disappear.
    • The use of scientific notation for chromosome position would cause errors when loading .seg files.

IGV 2.0.27  released December 19, 2011

  • Enabled indexing of GTF files.
  • Bug Fixes
    • Fixed synchronization bug that could cause IGV to hang on loading sessions.

IGV 2.0.26  released December 7,  2011

  • Improved test for http byte-range compatibility in the client network evironment.
  • Added support for "name" parameter in launch URLs.
  • Added support for "merge" parameter when using launch.php
  • Bug Fixes
    • Could not create an "svg" snapshot from batch scripts and port commands.

IGV 2.0.23  released November 29,  2011

  • Bug Fixes
    • Files sometimes appear "out of order" when restoring sessions.
    • Restoring session with password-protected resources would prompt multiple login dialogs for the same host.

IGV 2.0.21  released November 20,  2011

  • Added new http link option,  "launch", which loads files into IGV if its already running, or launches IGV if not.
  • Changed stop codon color to red in gene track.
  • Bug Fixes
    • Restored limited backward compatibility for older session files (versions 1 and 2).

IGV 2.0.19  released November 14 2011

  • Bug Fixes
    • Entering an illegal locus string (for example chr1:<space>100-200) in the search box could cause IGV to freeze.

IGV 2.0.18  released November 10 2011

  • Bug Fixes
    • New IGV installs would not start-up without a network connection.

IGV 2.0.17  released November 5 2011

  • Bug Fixes
    • "Go" command failed when chromosome names contain colons.
    • MAF file parser failed if file includes version number.
    • Closing port socket from a client disabled port.

IGV 2.0.15  released October 28 2011

  • Bug Fix
    • Heatmap scale could be wrong for certain datasets loaded from portals.

IGV 2.0.14  released October 23 2011

  • Base mismatch determination in alignments now account for IUPC ambiguity codes in the reference sequence.
  • Bug Fixes
    • "New" session was not releasing file handle.
    • Popup text often ceases working, requiring a forced screen refresh to reappear.

IGV 2.0.12  released October 13 2011

  • Bug Fixes
    • Loading GATK VCF files would sometimes fail with "error 416" or "illegal argument exception".
    • Coverage plots would sometimes show bars where there is no data.

IGV 2.0.11  released October 11, 2011

  • IUPAC ambiguity codes are now supported in BAM files
  • Gene lists (split screen view) can be created on-the-fly by entering multiple genes or loci in the search box.
  • Batch "goto" command can now take multiple loci, separate by spaces. 
  • Bug Fixes
    • Popup (tooltip) text would sometimes die, requiring a restart.
    • Searching for loci with "|" characters in the chromosome names would not work.

IGV 2.0.10  released September 24, 2011

  • Flagging of zero-quality alignments can now be disabled from the Preferences window.
  • A new track line option has been added to specify that exons be rendered in alternating colors. This is useful for situations where exons are adjacent, with no intervening introns, for example when viewing data against a transcriptome reference.  Example;
    • track name="Test alternate color" color=0,150,0 altColor=0,0,150 alternateExonColor=on
  • Multiple loci can now be specified in the "search" box and batch "goto" commands.  Each gene name of locus is separated by a vertical bar,  e.g.   egfr|pten.  The result will be a multi-locus (split screen) view.
  • You can now change genomes by loading indexed fasta files (.fai indeces) from "File > Load Genome...". 
  • Changes were made to the processing of batch and port commands to lessen the likelihood of blank snapshots.
  • The header panel can now be optionally hidden (from View menu).
  • Bug Fixes
    • The maxHeightPixels track line attribute was not correctly parsed.
    • Several bugs fixed affecting access to IGV servers from proxies.

IGV 2.0.9.  released August 21 2011

  • Added option to disable drawing of center line on alignment tracks.
  • Added batch command to define region of interest: example "region chr1:100-200".
  • Changed "sort by base" behavior for splice junctions. Alignments which span a base with a splice (i.e. do not actually cover the base) now appear at the bottom.
  • Bug Fixes
    • Basic Authentication would fail for some IIS servers with the error "File not found: ... .ini".
    • Sorting by attribute would not work if attribute column contained only a single non-null value.
    • BigWig files did not work with chromosome alias definitions.
    • Searching by "systematic name" in GFF files did not work.

IGV 2.0.8, released August 5 2011

  • Bug Fixes
    • Loading of sample information files from the Broad server would fail with a "Socket closed" error.

IGV 2.0.7, released August 3 2011

  • Added support for annotating VCF sample rows with metadata from a sample info file. This can be used, for example, to group samples by pedigree or population.
  • Fixed some performance bugs affecting HTTP access to large files.
  • Added support for NTLM Proxy authentication. NOTE: Please contact us if you use this, we need partners to help us test this.
  • VCF 4.1 is now fully supported. Also restored support for VCF 3.x.

IGV 2.0.6, released July 22 ,2011

  • The "fit data to window" function was tweaked to better fill available space.
  • Bug Fixes
    • TDF files did not work properly with chromosome alias definitions.
    • Alignments with "weird" pair orientations were not colored properly if the inferred insert size was < the read length.
    • Alignment coverage tracks were not properly resored from session files.

IGV 2.0.5, released July 13 ,2011

  • Bug Fixes
    • BigWig data could show up on chromosomes not in original WIG file, in some circumstances.

IGV 2.0.4, released July 12 ,2011

  • Goby alignments are now rendered with lines connecting parts of reads that span exon-exon junctions.  Alignments with splicing information can be generated for RNA-Seq data with GSNAP compiled with Goby support. Splicing information is automatically detected when present and displayed. [see an example here]
  • Colors can now be assigned to attribute values in sample information files.  Single or two color scales can be associated with numeric columns.   For more details click here.
  • Bug Fixes
    • VCF records with less than two alleles would cause stack trace error.
    • Null pointer exception error when loading .cn and .igv files with unrecognized chromosomes.
    • Popup menus and tooltip text would remain when IGV window looses focuse (Mac OS). 

IGV 2.0.3, released June 22, 2011

  • BigWig and BigBed formats are now supported.  File extensions must be either (case insensitive):
    • BigWig:  bw or bigwig
    • BigBed:  bb or bigbed
  • Background color can now be set (View > Preferences > General tab).
  • Bug Fixes
    • Zoom (+) button did not work on wide displays.
    • IGV froze when browsing over left edge of chromosome. This condition could occur if "show soft-clipped bases" is on.
    • Panning by "dragging" with the mouse was not working on Linux or Windows computers.

IGV 2.0.1, released June 13,  2011

  • Genomic coordinates of current exon appear in hover text.
  • Goby ".counts" files for coverage data is now supported.
  • VCF tracking rendering changes:
    • Consistent color scheme now used in variant display row (the top row) for files with or without genotypes:
      • blue - minor allele frequency/fraction is known (from annotation or genotype data)
      • grey - minor allele frequency is not known
      • red - height is proportional to minor allele frequency
    • User can now set height of "squished" rows
    • Track responds to "fit data to window" button by adjusting squished row height, within limits
  • New user preference to display region boundaries (under General tab)
  • Bug Fixes 
    • Chromosome aliases do not work in search text.
    • Expanded feature tracks could occasionally drop last row.
    • Cannot sort or filter on track name after using "rename" function.
    • Gene and other annotation tracks sometimes disappear after sorting.Sorting by attribute does not work unless all three sort fields are used

IGV 2.0, released  May 31, 2011.

  • New file formats, including Cufflinks files, Goby, GWAS, and VCF, as well as custom file formats and a merged BAM file format
  • New toolbar features, including the back and forward buttons, and the Fit-to-Window button
  • New NGS functionality, including a split screen view, a view as pairs option, viewing splice junctions, and coloring by insert size
  • The ability to view GWAS data
  • An option to create/import and view gene lists
  • Options for viewing VCF files
  • New sequence track and feature track options
  • A "Region of Interest" navigator

See the IGV 2.0 section of the User Guide for details.