IGV - is there a way to extract bulk information?
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!
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Chris Miller
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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
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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
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!
To build on Pierre's comment, there is a Python script here to facilitate the process: https://github.com/stevekm/IGV-snapshot-automator
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).
This recent Biostars post may also be useful.