Question: IGV - is there a way to extract bulk information?
2
gravatar for blur
9 months ago by
blur90
European Union
blur90 wrote:

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!

igv • 393 views
ADD COMMENTlink modified 9 months ago by Chris Miller20k • written 9 months ago by blur90
2

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

ADD REPLYlink written 9 months ago by Pierre Lindenbaum115k

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!

ADD REPLYlink written 9 months ago by blur90

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

ADD REPLYlink written 9 months ago by steve1.8k

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

ADD REPLYlink written 9 months ago by Hussain Ather890

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).

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax59k

This recent Biostars post may also be useful.

ADD REPLYlink written 9 months ago by erwan.scaon590
1
gravatar for Chris Miller
9 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

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

ADD COMMENTlink written 9 months ago by Chris Miller20k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1605 users visited in the last hour