IGV 2.2 released December 18, 2012

• Improved interface for loading and managing genomes. In previous releases, the genome drop-down menu listed all genomes that are available in IGV. However, the list of hosted genomes has grown beyond the point where it is manageable in a single dropdown. In IGV 2.2 you can customize the drop-down menu to include only the genomes that are of interest to you. The genome menu now initially lists only a small number of default genomes, but you can add genomes to the list, remove genomes from the list, and rearrange the order of genomes in the list. See Managing and Loading Genomes in IGV 2.2.

• Integration with BEDTools. BEDTools is a fast, flexible suite of tools that can be used to compare sets of genomic features. IGV can now use BEDTools to compare features in loaded tracks, and view the results as a new track. See BEDTools Integration. Note: This is currently not supported on Windows

• Integration with GenomeSpace. GenomeSpace is a system that bridges the gaps between bioinformatics tools, making it possible to move data smoothly between tools, leveraging the available analyses and visualizations in each of these tools. IGV is one of the founding tools in the GenomeSpace initiative. See IGV and GenomeSpace.

• New menu bar layout. The main IGV menu bar layout has been updated to accommodate the new features described above. There are now three new items in the menu bar:
  • Genomes. Items related to loading and managing genomes have been moved out of the File menu, and into their own menu.  
  • Tools. Items related to external tools have been moved out of the File menu, and into their own menu. Use the Tools menu to run the BEDTools functions, igvtools, and IGV batch scripts .
  • GenomeSpace. Items related to GenomeSpace are in their own menu.

• Network view. IGV can now connect to the cBio Cancer Genomics Portal to display information about networks of genes. An IGV gene list is used to provide seed genes to the cBio portal, which then displays a network of the seed genes and their neighboring genes. You can filter the network based on mutation, copy number, and expression data that you have loaded into IGV. See Viewing Gene Networks in the cBio Portal.

• Alternate coding sequence translations. When the view is zoomed in to display individual nucleotide bases in the sequence track, IGV displays the 3-frame translation to the corresponding amino acid sequence. You can now select from 18 alternate NCBI translation tables. Enable this view and select the translation table by right-clicking on the sequence track.

• New option for pop-up details.  By default, when you hover over an element in the data panel you will see a pop-up display with details about the element. You can now choose to only display the details when you click on the element. You can also disable the pop-up so that it is not displayed at all. Click on the yellow balloon icon in the IGV tool bar to specify the behavior you want.

• New options for grouping sequence alignments. Two new options have been added to the menu for grouping alignments: for paired alignments, you can now group by mate chromosome or pair orientation.

• New file formats. IGV now supports GenBank (.gbk) files, and the ENCODE narrowPeak and broadPeak formats. The GATK reduced read form of BAM files is now also supported.
  • Starting with GATK 3.0 in March of 2014, ReduceReads was discontinued due to inferior quality issues as described in this GATK blog post.

• New in sessions. IGV sessions now use relative file paths, by default.

• New batch command. When controlling IGV through a port or a batch script, you can now set the data range of tracks with the setDataRange command.

• New in igvtools. 
  • New options for the count command: --strands and --bases. 
  • Indexing of FASTA files.
  • Improved performance in the sort command.
  • See the igvtools documentation for details.

 IGV 2.2.2    Jan 7, 2013

Bug Fixes:

• Whole-genome view not displayed correctly for TDF files.
• Paths to fasta files not parsed correctly on Windows OS leading to "file not found" error when creating .genome files.

 IGV 2.2.4    Jan 14, 2013

New user preference added on the "Advanced" tab to disable anti-aliasing.  This can significantly improve performance in some circumstances with running with X-Windows.

Bug Fix:

• GFF3 features with unspecified strand drawn incorrectly.

IGV 2.2.5   Jan 25, 2013

Bug Fix:

• "Null pointer exception" when using merge option in html links.

IGV 2.2.6   February 19, 2013 

Bug Fixes:

• Amino acid translations not shown from GFF files (reading frame was not being read).
• Loading fastas with very large integers for chromosome names fail.
• Whole genome views for certain TDF files are not shown.

IGV 2.2.7   February 25, 2013 

Bug Fix:

• Filtering tracks based on sample information also removes gene annotations.

IGV 2.2.8   February 28, 2013 

Bug Fix:

• IGV would fail to start up if last used genome was not reachable.

IGV 2.2.9   March 10, 2013 

• Set autoscale to false when data range is manually set.
• Adjust scale threshold at which insertions are shown

IGV 2.2.11   March 16, 2013 

• Include insertions when sorting alignments by base.
• Enable settting of sample ID from Resource element in load xml.

Bug Fixes:

• First data points of a chromosome are ignored when computing whole genome view under some conditions.
• GenomeSpace paths with spaces were not loading due to premature url decoding of parameters
• Genomes with large #s of contigs were not loading in some situations.
• IndexArrayOutOfBounds exception in Goby alignment files.

IGV 2.2.12   March 18, 2013 

Bug Fix:

• Auto-generated TCGA sample names are not recognized.

IGV 2.2.13   March 22, 2013 

Bug Fix:

• "tanscript_id" is not recognized as a name field in GTF files.