IGV 1.3

New in this release

IGV 1.3, released May 2009, includes the following new features and improvements:

  • View sequence alignments. Sequence alignments in SAM and BAM file formats (http://samtools.sourceforge.net/) can now be viewed in IGV. See Alignment Data for details. Use File>Load from Server to view sample datasets from the 1000 Genomes project (http://www.1000genomes.org). Note that BAM files must be indexed, and SAM files must be orderd by alignment start location. It is reccommended that large SAM files be converted to BAM format prior to viewing. IGV also provides limited support for alignments in the sorted.txt output from the Illumina Pipeline Version 1.3. See Illumina Sequencing Support for details.
  • Enhanced RNAi support. IGV now includes enhanced support for loading and viewing RNAi datasets based from the RNAi Consortium shRNA library (http://www.broad.mit.edu/node/297). See RNAi Data for details.
  • Enhanced gene expression support. IGV now includes the option to map expression data to the chromosome using probe locations (when available) rather than genes. See Expression Data for details.
  • New display features. With this release, IGV adds a number of new features including the ability to rename tracks, rearrange tracks via drag-and-drop, search for tracks by name, and display track data using line plots.
  • Performance improvements. IGV loads and displays all ASCII file formats (bed, wig, gct, igv, cn) significantly faster.
  • Additional genomes. The following genomes have been added to the IGV genome server since the December 2008 release of IGV 1.2: Human assembly b36 (the reference genome for the 1000 Genomes project), Plasmodium falciparum assembly 3D7 v5.5, C. elegans assemblies ce6 and ce4, D. melanogaster assemblies dm3 and dm2, and O. Sativa release 6. For a current list of supported genomes, click the genomes drop-down list in the IGV tool bar.