The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. Features include:
- Support for a wide variety of data types including
- Genetic variation (copy number, loss of heterozygosity, somatic mutations)
- Gene/microRNA expression
- RNAi screens
- Epigenetic data
- Genomic annotations
- Sequence Alignments
- Easy access to genomes and datasets hosted by the Broad Institute
How to Use
This application requires an X-Windows connection.
IGV uses environment modules. Typemodule load igv
at the prompt. Then typeigv
There are two options available.
- -m or --memory memory allocated
- -t or --tmpdir temporary directory
By default, IGV uses 1gb of memory and uses /scratch/$USER/igvtmp as the temporary directory, where $USER is the login of the user running IGV. To allocate 20gb of memory, use:igv --memory 20g
Input/output for IGV is menu-driven through the GUI:
IGVTools allows commandline utilities for working with ascii file formats.
- tile converts a sorted data input file to a binary tiled data (.tdf) file. Supported input file formats: .wig, .cn, .snp, .igv, .gct
- count computes average alignment or feature density for over a specified window size across the genome. Supported input file formats: .sam, .bam, .aligned, .sorted.txt, .bed
- sort sorts the input file by start position. Supported input file formats: .cn, .igv, .sam, .aligned, and .bed
- index creates an index file for an input ascii alignment or feature file. Supported input file formats: .sam, .aligned, .sorted.txt, and .bed
To use IGVTools, type
module load igvtools
at the prompt. Then type
IGVTools is also available as a GUI. Type
at the prompt.
By default, IGVTools uses 5gb of memory and the same temporary directory method as IGV. To allocate 20gb of memory, use:
igvtools --memory 20g [ additional options for igvtools ]
To see what options are available for the commandline IGVTools, just type igvtools at the prompt:
Program: igvtools. IGV Version 2.2.2 (5)03/06/2013 06:46 PM Usage: igvtools [command] [options] [input file/dir] [other arguments] Command: version print the version number sort sort an alignment file by start position. index index an alignment file toTDF convert an input file (cn, gct, wig) to tiled data format (tdf) count compute coverage density for an alignment file formatexp center, scale, and log2 normalize an expression file gui Start the gui help
display this help message, or help on a specific command See http://www.broadinstitute.org/software/igv/igvtools_commandline for more detailed help