New in this release
IGV 1.2, released December 2008, includes the following new features and improvements:
- Additional genomes. Genomes are continually being added to the IGV genome server. As of this release, IGV supports the following genomes: Human (hg18, hg17, hg16), Mouse (mm9, mm8, mm7, mm6, mm5), Chicken (galGal3), Plasmodium (3D7 v2.1), Yeast (S. cerevisiae, S. pombe), Zebrafish, Neurospora crassa (v3), and T. castaneum (2.0). For a current list of supported genomes, click the genomes drop-down list in the IGV tool bar.
- Import genomes. Genomes that are not yet available on the IGV genome server, can now be imported into IGV. To import your favorite genome, click File>Import Genome. See Loading a Genome for details.
- Support for probe identifiers. When loading a GCT or RES file, IGV now recognizes Affymetrix, Agilent and Illumina probe identifiers and automatically places the gene expression data at the correct loci. See Expression Data for details.
- Search feature tracks. The search box in the IGV tool bar now allows you to search for a locus (for example, chr5:90,339,000-90,349,000), gene (for example, DPYD), or any feature in a feature track (for example, NM_10000000).
- New display options. IGV displays track data using a heatmap, bar chart, or scatter plot. IGV now provides several additional display options for bar charts and scatter plots. See the Charts tab of the Preferences window for details.
- General Feature Format (GFF) file support. IGV can now load genomic features from GFF2 or GFF3 files. For IGV, use the .gff file extension for GFF2 and the .gff3 file extension for GFF3 files. See the Wellcome Trust Sanger Institute web site (http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml) for a description of the GFF2 file format. See the Sequence Ontology Project (SO) web site (http://www.sequenceontology.org/gff3.shtml) for a description of the GFF3 file format.
- Wiggle (WIG) file support. IGV can now load a feature or data track from a wiggle (WIG) file. The file must have a .wig file extension. See the USCS Genome Bioinformatics web site (http://genome.ucsc.edu/FAQ/FAQformat) for a description of the wiggle (WIG) file format.