IGV 1.4

New in this release

IGV 1.4.2, released February 5, 2010

  • Fixed performance bug affecting BAM files
    • Users outside of the Eastern US region should see performance improvements when browsing BAM files with Broad hosted genomes 
  • FIxed a bug that caused chromosomes/contigs for imported genomes to be scrambled.
  • Added support for controlling IGV sessions from http links.

IGV 1.4.1,  released December 16, 2009

  • Performance improvements for large .wig files
    • The memory required to load large .wig files has been reduced. 
  • SAM/BAM validation stringency has been relaxed.
    • This change enables viewing of many SAM/BAM files that are not strictly compliant with the SAM specification.
  • Faster startup time. 
  • New port command options for sorting.
  • Support for the 1KG low coverage data.
  • Alignments may now be colored by read strand.
  • Fixed in genome importer that sometimes caused the last chromosome to be dropped fixed.
  • IGVTools
    • The tile and count commands now support data compression.  Use the -c option to compress output files.
    • The tile command now supports mapping of probes to locations with a user supplied .bed file.

IGV 1.4, released October 2009, includes the following new features and improvements for alignment tracks:

  • New alignment track options:
    • Two menu items have been added to the alignment popup menu. Go to mate region jumps to the region of the paired read (if any). Show all bases displays all bases in a read regardless of whether they are mismatched.
    • The Sort alignments menu item includes several new options: by base and by sample, by strand, and by read group.
  • Highlight paired reads. Control+click (Mac: Command+click) a read to outline the read and its paired mate. Colors are arbitrary but unique to each pair. A black outline indicates that the selected read has no mate. To clear all outlines, right-click and select Clear selections from the alignment popup menu.
  • Alignment shading. IGV offers a display option that shows a line at the center of the display and shades alignments that intersect the center line. That display is now optional. Use the Alignments tab of the Preferences window to select (or clear) the option to Shade alignments intersecting at center.
  • Coverage track. Each alignment track is now supplemented by a coverage track.  By default this track displays coverage from loaded alignment data.  In addition, pre-calculated coverage in the form of a .tdf file can be displayed when available.   The track displays the depth of the reads displayed at each locus as a gray bar chart. At loci where greater than 20% of the quality weighted reads do not match the reference IGV colors the bar in proportion to the read count of each base (A, C, G, T).  
  • Reference sequence. By default, IGV displays the reference sequence once. Select the Show Reference Sequence option on the Alignments tab of the Preferences window to display the reference sequence with each alignment track. Modifying this option affects the display of subsequently loaded alignment tracks.
  • Maximum read depth. The maximum depth of reads displayed at any given locus has been increased from 1,000 to 100,000. To modify this setting, use the Maximum read depth option on the Alignments tab of the Preferences window.
  • Filter read groups. Use the new Filter alignments option on the Alignments tab of the Preferences window to hide alignments that match specified read groups.  To use this option you must specify a url or absolute file path to a flat file containing a list of read groups to filter. 

In addition:

  • The File menu now provides an option to load data files from URL, as well as from the file system or data server.
  • File>Load From Server now filters the list of available datasets based on the genome currently selected in IGV.
  • The track pop-up menu provides a new option (Set Heatmap Scale) to modify heatmap settings for selected copy number, expression and methylation data tracks.
  • Most file formats now allow a track line for setting display options.
  • There is a new user preference under the General tab to enable or disable automatic zooming when searching by feature.
  • IGV can now be launched and controlled through HTML links.
  • The IGV web site was redesigned and the documentation reorganized to provide better access to information. We welcome your comments and suggestions.