Tool: Automatic IGV snapshot script
gravatar for steve
2.5 years ago by
United States
steve2.2k wrote:

I've been using IGV batchscripts to create automated programmatic snapshots of genome coverages and variants for ChIP-Seq and whole exome samples, and thought it would be helpful to have a stand-alone script that handled this. So I put together this IGV Snapshot Automator:

Just put the regions you want to take snapshots of in the 'regions.bed' file, and pass the files you want visualized as arguments. The script will handle the rest. It also has some options for specifying different regions files, memory settings, track height, reference genome, and IGV binary location (in case you've already got it installed elsewhere).

The best part of this is that it can run headlessly on your Linux server, where the data reside. See the notes in the repo for details.

Example output:


igv tool chip-seq tutorial • 2.9k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by steve2.2k

I've forked the project. It works. +1. Well done!

ADD REPLYlink written 2.5 years ago by SmallChess490
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