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Sample Batch Script for IGV Snapshots
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igv_test_bat.md

Manual page here:

http://software.broadinstitute.org/software/igv/batch

These commands are also available:

http://software.broadinstitute.org/software/igv/PortCommands

After installing IGV, a script can be run from the terminal. Sample script (save this as IGV_test.bat):

new
snapshotDirectory /path/to/snapshot_dir
load /path/to/sample1.bam
load /path/to/sample2.bam
genome hg19
maxPanelHeight 400
goto chr11:108138003-108138003
snapshot custom_chr11-108138003-108138003.png
goto chr9:21971111-21971111
snapshot custom_chr9-21971111-21971111.png
exit

Example command to run IGV:

bin/IGV_2.3.81/igv.sh -b code/IGV_test.bat
@jimguo
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jimguo commented Apr 22, 2019

Hi, how did you load multiple bed files? Thanks.

@ShwetaCh
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ShwetaCh commented Nov 3, 2020

Is there a way to size to snapshot in a landscape mode? It gives me a portrait mode image. Thanks.

@stevekm
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stevekm commented May 31, 2025

@jimguo see the repo here https://github.com/stevekm/IGV-snapshot-automator but you likely want this instead https://github.com/igvteam/igv-reports

@ShwetaCh the dimensions are related to the size of the xvfb buffer that gets used, I think there are some args you can try to use to control it

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