IGV and IGVTools
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:
The following versions are installed and currently available...
... on environment hpc-env/8.3:
... on environment hpc-env/6.4':
... on environment hpc-uniol-env:
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
The full documentation of IGV and IGVTools can be found here.