Integrative Genomics Viewer

Category Genomics>Genetic Data Analysis/Tools

Abstract The Integrative Genomics Viewer (IGV) is a fast, flexible viewer for genomic data.

Products features/capabilities include:

1) IGV visually integrates datasets from various platforms and sources, including --

• a) Genetic variation data (copy number, loss of heterozygosity, mutations);
• b) Gene/microRNA expression data;
• c) Epigenetic data;
• d) RNAi screens;
• e) Genomic features;
• f) Clinical and phenotype annotation of samples.

2) IGV efficiently handles whole genome data files. You can load data from several experiments for side-by-side comparisons and easily zoom from genome to chromosome to base pair resolution.

3) IGV displays any feature or data that can be mapped to genomic coordinates. It supports several file formats for loading genomic features and data.

At the most basic level, genomic features (such as genes) are labeled at chromosomal locations and genomic data (such as gene expression data) are values associated with such features.

4) Genome and Chromosomes -- By default, IGV selects the human (hg18) genome, loads gene annotations into the feature panel, and displays chromosome 1.

IGV currently provides sequence data for the following genomes: hg17, hg18, mm8, and mm9.

5) Tracks and Attributes -- IGV displays genomic data and annotations in horizontal rows called 'tracks' (see below). IGV offers several alternative display options (see below).

By default, IGV displays feature tracks (for example, genes) in the feature panel and data tracks (for example, gene expression data) in the data panel.

Note: The feature and data panels can be combined into a single panel.

IGV displays sample information in an attribute heat map. IGV also offers several attribute display options which can be turned on or off.

6) Preprocessing Data Files -- Preprocessing a data file computes the data that will be displayed at selected zoom levels and stores the results in a smaller binary (.h5) file. Most data files can be loaded into IGV without preprocessing.

For large files, however, preprocessing significantly improves the speed at which IGV loads and displays the data. As a general rule, files with more than 250,000 rows should be preprocessed.

You can preprocess a data file in IGV or run the IGVPreprocess module in Gene Pattern (see G6G Abstract Number 20183). Using the Gene Pattern module allows you to continue working while preprocessing large data files.

7) Display Options for Tracks -- IGV provides several track display options, which can be set per track, per attribute value, or by preference (see below).

8) Tracks -- A track is a row of data displayed in IGV. Each track consists of a track identifier and associated data. A track can be characterized as a feature track or a data track based on the data that it contains:

• a) A 'feature track' contains labels, such as gene names.
• b) A 'data track' contains numeric values, such as gene expression data or copy number data.

9) Preference options include:

• a) Distinguish missing data: Bar chart and scatter plot only. By default, IGV does Not distinguish between zero values and missing data.
• b) Combine data and feature panels: By default, IGV displays data tracks (e.g. expression data) in one panel and feature tracks (e.g. genes) in another.
• c) Join adjacent copy number segments: By default, IGV leaves gaps between adjacent copy number segments. This option can be selected to fill the gaps between adjacent segments by extending the segment endpoints.
• d) Show attribute display: By default, IGV shows attributes and attribute values to the left of the data panel.
• e) Enable regions of interest: By default, IGV shows the ‘Define a region’ icon.
• f) Default track height: By default, each track is 20 pixels high.
• g) Draw exon numbers in Gene track: Select this option to display exon numbers in the Gene track.
• h) Track name attribute: Override the default track name selected by IGV by entering the name of the attribute IGV should use as the track name attribute.
• i) Display mutation data as distinct tracks: By default, IGV displays mutation tracks as separate tracks (in addition to overlaying them).
• j) Enable image caching: By default, IGV enables image caching to improve performance. We recommend leaving this option selected.

10) Overlaying Mutation Data -- A mutation track displays variant bases. In the mutation (.mut) track file, each row identifies a mutation by chromosome, locus, and sample or patient ID.

In IGV, the track name for a mutation track is the sample or patient ID and the track displays the mutations for that sample or patient:

The overlay feature allows mutations to be examined in the context of other data, such as gene expression or copy number data. If a mutation track and a data track have the same value (for example, if they represent data from the same patient), IGV overlays the two (2) tracks.

IGV displays the mutation track overlaid on the data track and also as a distinct track. By default, IGV displays mutation data both ways.

System Requirements

IGV is a desktop application for Windows and Mac OSX.

Manufacturer

• Broad Institute of MIT and Harvard
• 7 Cambridge Center
• Cambridge, MA 02142
• Ph: 617.452.3000
• Fax: 617.452.4588
• or
• 320 Charles Street
• Cambridge, MA 02141-2023
• Ph: 617.258.0900
• Fax: 617.258.0901
• E-mail: igv-help@broad.mit.edu

Manufacturer Web Site Integrative Genomics Viewer

Price Contact manufacturer.

G6G Abstract Number 20226

G6G Manufacturer Number 101795