Niknafs / IGV-snapshot-automator

Script to automatically create and run IGV snapshot batcscripts

IGV Snapshot Automator

A script to automatically create and run IGV snapshot batchscripts. This script will first write an IGV batch script for the supplied input files, then run IGV headlessly (no GUI shown) and take snapshots at the locations defined in the regions.bed file.

Designed for use on Linux systems.

Usage

Download a copy of IGV

$ cd bin
bin$ ./get_IGV.sh

Create and run batchscript:

$ python make_IGV_snapshots.py /path/to/alignments.bam

Make batchscript but don't make snapshots:

$ python make_IGV_snapshots.py /path/to/alignments.bam -nosnap

See python make_IGV_snapshots.py --help for more available options

Example Output

Notes

Default memory allotment is set at 4GB; this can be changed with the -mem argument (e.g. -mem 1000 sets memory to 1GB).

IGV may take several minutes to run, depending on the number of input files and regions to snapshot. Stdout messages from the program may not appear immediately in the console.

Software Requirements

• Python 2.7 or 3+
• bash version 4.1.2+
• IGV (download script provided in bin directory)
• Xvfb
• xdpyinfo
• Java runtime environment