Tool: Automatic IGV snapshot script
8
gravatar for steve
8 months ago by
steve1.1k
United States
steve1.1k 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:

https://github.com/stevekm/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:

chr1_713500_714900_h500

igv tool chip-seq tutorial • 698 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by steve1.1k

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

ADD REPLYlink written 8 months ago by student-t410
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