IGV Early Access Guide

Early versions of new features are made available in the early access version of IGV before they are officially released. You can install this version from the early access download page on the IGV web site. This guide describes what's new in IGV Early Access (141, December 11, 2012) since IGV Release 2.1. 

New Features 

  • 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 managable 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 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.