IGV and IGVTools

Introduction

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

The IGVTools utility provides a set of tools for pre-processing data files. File names must contain an accepted file extension, e.g. test-xyz.bam. Tools include:

• toTDF
• count
• index
• sort

Installed version

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• IGV/2.3.80
• IGV/2.11.1-Java-11
• IGVTools/2.3.75
• IGVTools/2.4.19-Java-11

... on environment hpc-env/6.4':

• IGV/2.3.80
• IGV/2.11.1-Java-11
• IGVTools/2.3.75
• IGVTools/2.4.19-Java-11

... on environment hpc-uniol-env:

• IGV/2.3.80
• IGV/2.11.1-Java-11
• IGVTools/2.3.75
• IGVTools/2.4.19-Java-11

Loading / Using IGV and IGVTools

To load the desired version of the module, use the module load command, e.g.

module load IGV/2.11.1-Java-11
## and/or
module load IGVTools/2.4.19-Java-11

Always remember: this commands are case sensitive!

To find out on how to use IGV you can just type in igv.sh --help to print out a help text to get you started:

$ igv.sh --help
Using system JDK.
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11.0.2" 2019-01-15
OpenJDK Runtime Environment 18.9 (build 11.0.2+9)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.2+9, mixed mode)
Command line options:
Space delimited list of data files to load
--preferences, -o  Path or URL to a preference property file
--batch. -b  Path or url to a batch command file
--port, -p  IGV command port number (defaults to 60151)
--genome, -g  Genome ID (e.g hg19) or path or url to .genome or indexed fasta file
--dataServerURL, -d  Path or url to a data server registry file
--genomeServerURL, -u  Path or url to a genome server registry file
--indexFile, -i  Index file or comma delimited list of index files corresponding to data files
--coverageFile, -c  Coverage file or comma delimited list of coverage files corresponding to data files
--name, -n  Name or comma-delimited list of names for tracks corresponding to data files
--locus, -l  Initial locus
--header, -H http header to include with all requests for list of data files
--igvDirectory Path to the local igv directory.  Defaults to <user home>/igv
--version  Print the IGV version and exit
--help Print this output and exit

To find out on how to use IGVTools you can just type in igvtools help to print out a help text to get you started:

$ igvtools help
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2021-10-07T13:23:42,988]  [Globals.java:138] [main]  Development mode is enabled

Program: igvtools. IGV Version 2.4.19 02/15/2019 01:11 AM

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 <command>     display this help message, or help on a specific command
	 See http://www.broadinstitute.org/software/igv/igvtools_commandline for more detailed help
	
Done

Documentation

The full documentation of IGV and IGVTools can be found here.