This module is currently in beta release. The module and/or documentation may be incomplete.

Launches the Integrative Genomics Viewer (IGV) with the provided file and input parameters.

Author: Barbara Hill, Marc-Danie Nazaire, Jim Robinson, Peter Carr (Broad Institute)

Contact: gp-help@broadinstitute.org

Algorithm Version:


This module launches IGV on a specified data file or IGV session file. For full documentation and more information about IGV, please visit the IGV website. (http://broadinstitute.org/igv). Each run of the module creates a Java WebStart file named igv_job_<gp_job_id>.jnlp. A corresponding launch button is also displayed on the IGV job status page. Click on this button to launch IGV. Note that in some Web browsers you must download the file, and then directly launch it from your client computer. The launcher automatically installs or updates to the latest released version of IGV.IGV will prompt you for your GenePattern username and password before it opens the data or session file. Once you have IGV running, you can also directly open GenePattern files by selecting File>Load from URL… from the IGV menu and entering the URL of the GenePattern file. Right-click (CTRL-click on the Mac) on a filename in GenePattern to copy the URL link address and then paste it into the IGV URL entry box. Note that accessing your GenePattern files from IGV will only work with GenePattern Server versions 3.3.2 or later.


Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.  Briefings in Bioinformatics 2012.

James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011).


Name Description
[parameter name] [parameter description] Default: [value]

* - required

Input Files

  1. [parameter name]
    [Description. For example: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the GenePattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.

Output Files

  1. [File name]
    [Description of the content, file format, and how to interpret the results.]

Example Data

[provide example data, including input files and parameter settings]. (we’ll put the input files on the ftp site and link to them from the doc)


[any software requirements for running this, e.g., version of R, licensing]

Platform Dependencies

Task Type:

CPU Type:

Operating System:


Version Comments

Version Release Date Description