IGV 2.8.x

IGV 2.8.0, released January 2020

This release includes the following new features and improvements:

1. Sequence alignment tracks

  • A number of default values are set based on the sequencing experiment type, which is inferred from the alignments when they are first loaded from the file, i.e., when the view is sufficiently zoomed in to a region that contains alignments. The alignment track popup menu now includes a new item where the experiment type can also be set explicitly. Values include: 'RNA', '3rd Gen', and 'Other' (the default). (Git issue #736). Note that any values that are set based on experiment type can be overriden in the preferences (View > Preferences).
  • The Copy read sequence command in the track popup menu is now available when viewing alignments as pairs. (Git issue #580).
  • Sorting alignments by start position now uses the first mapped base and ignores any soft-clipped bases. (Git issue #725).
  • Fixed an issue with the read details presented in the popup text for read string = "*". The length was incorrectly presented as 1bp; it is now reported as "undefined". (Git issue #557).
  • The Alignments tab of the Preferences window has a new option to specify the default display mode for alignment tracks. It can be set to EXPANDED, SQUISHED, or COLLAPSED. The display mode for an individual track can be changed via its popup menu. (Git issue #134).  
  • The option to filter alignments by read group is back in the Alignments tab of the Preferences window. It had inadvertently been dropped in a previous release. 

2. Translation view in reference sequence track

  • Coloring of start codons was previously based on the amino acid, not the codon. This meant that Methionine (M) was colored green whereever it was found, which is not always correct (e.g. for the Mitochondrial table). Now AUG/ATG are colored green. In addition, the genetic code tables can now include alternative start codons that are colored yellow. Specifically, for Vertebrate Mitochondria these are AUA, AUU, and AUC.  (Git issue #582). 
  • In previous releases, the amino acids in view were not always updated when a different translational table was selected. This has now been fixed.

3. Sample attributes

  • New feature: Overlay tracks based on a shared sample attribute via Tracks > Overlay. (Git issue #396).  
  • New feature: Rename tracks based on a sample attribute via Tracks > Rename. (Git issue #681). 
  • Renaming a track via the popup menu no longer disables its sample attributes. The attribute key is now the original track name, and so the track retains its sample attribute assignments when it is renamed. 
  • Coverage and splice junction tracks for a .bam file are now assigned the same sample attribute information as the associated alignment track. (Git issue #524).  
  • Reinstated the option to specify a sample attribute key to use for track names by default. This option was inadvertently dropped from the Tracks tab of the Preferences window in a previous release.
  • Fix to allow the #sampleMapping section to stand alone in a separate text file. The behavior now matches the description in the user guide. (Git issue #523).  

4. Other new features and improvements

  • Resize an existing Region of Interest by CTRL-clicking on its red region bar below the genome ruler and dragging to the new start or end position. (Contributed pull request #723)
  • Change the view locus by dragging the red box in the cytoband view. (Git issue #674). 
  • Add a new empty data panel to the display via View > Add New Panel. Move tracks into the panel by selecting the track names and dragging them to the new panel. (Git issue #258). 
  • dbSnp searches are now supported for the following assemblies. Enter the SNP's RSID, e.g. rs172334, into the locus search box. (Git issue #477).
    • Human hg19 and hg38; dbSNP build 151 (source UCSC Browser)
      • Common SNPs, i.e. found in >= 1% samples
      • Flagged SNPs, i.e. rare, but flagged as clinically associative by dbSNP
    • Mouse mm10; dbSNP build 142 (source UCSC Browser)
      • Common SNPs, i.e. found in >= 1% samples
  • New file type: Files of type regionPeak are now supported and are treated the same as narrowPeak files.
  • New options when running IGV from the command line  (Git issue #611).
    • --help will print a list of available command-line options and then exit.
    • --version will print the IGV version and then exit.
  • Fixed an issue with the display of read coverage in Sashimi plots. Sometimes the coverage seemed to disappear in zoomed out views. (Git issue #579). 

5. The menu that connected IGV to GenomeSpace has been removed. With the discontinuation of NHGRI funding for the GenomeSpace project its servers have now been shut down. See genomespace.org for more details.