IGV - is there a way to extract bulk information?

Question

[blur]

Hi,

I've been asked to check a few hundred areas in IGV. I was wondering if there is a way to extract images in bulk from it? They insist on visual information from IGV, not extracting information using pileup, samtools coverage etc - but just IGV. Anyone know how to do that? Thanks!

[Pierre Lindenbaum]

see the manual:

Running IGV with a batch file : https://software.broadinstitute.org/software/igv/batch

and /or

Controlling IGV through a Port https://software.broadinstitute.org/software/igv/PortCommands

see: Easy Way To Screenshot Whole Region From Igv? ; Hints For Integrating The Integrative Genomics Viewer (Igv) In Other Java Based Software? ; IGV command line control

[blur]

thanks, this works great! any idea how I can add more viewing parameters? or are only these options possible? specifically I'd like to set the allele frequency threshold https://software.broadinstitute.org/software/igv/PortCommands

Thanks!

[steve]

To build on Pierre's comment, there is a Python script here to facilitate the process: https://github.com/stevekm/IGV-snapshot-automator

[Hussain Ather]

Check out the export methods here REMINDER: 600 WORDS DEADLINE: APRIL 1 OR SOONER (for May-June issue of the NIH Catalyst)

[GenoMax]

Check out the export methods here REMINDER: 600 WORDS DEADLINE: APRIL 1 OR SOONER (for May-June issue of the NIH Catalyst)

In haste to be helpful you seem to have forgotten to include the actual link you intended to (and added some extraneous stuff from a previous unrelated copy operation).

[erwan.scaon]

This recent Biostars post may also be useful.

Answer 1

[Chris Miller]

My script here has some useful code if you're going to be submitting this to a cluster/running headless: https://github.com/chrisamiller/igvScreenshot