IGV batch scripts

Question

[bioinfo456]

Hi,

Hope all of you are doing good :)

This is a two part question,

1. I get the following error when trying to use hg38 to plot my bam files.

INFO [2021-06-30 11:29:58,978] [Main.java:154]  Startup  IGV Version 2.4.10 03/20/2018 10:50 PM
INFO [2021-06-30 11:29:59,015] [Main.java:155]  Java 10.0.2
INFO [2021-06-30 11:29:59,017] [DirectoryManager.java:76]  Fetching user directory...
INFO [2021-06-30 11:30:00,177] [Main.java:156]  Default User Directory: /home/urangasw
INFO [2021-06-30 11:30:00,179] [Main.java:157]  OS: Linux
INFO [2021-06-30 11:30:02,839] [Main.java:202]  A later version of IGV is available (2.9.4)
INFO [2021-06-30 11:30:31,788] [GenomeManager.java:186]  Loading genome: /home/urangasw/igv/genomes/hg19.genome
INFO [2021-06-30 11:30:40,862] [GenomeComboBox.java:79]  Enter genome combo box
INFO [2021-06-30 11:30:40,883] [GenomeManager.java:275]  Genome loaded.  id= hg19
INFO [2021-06-30 11:30:41,130] [CommandListener.java:120]  Listening on port 60151
INFO [2021-06-30 11:30:41,340] [BatchRunner.java:72]  Executing Command: new
INFO [2021-06-30 11:30:53,910] [CommandExecutor.java:235]  OK
INFO [2021-06-30 11:30:53,911] [BatchRunner.java:72]  Executing Command: genome hg38
INFO [2021-06-30 11:30:53,913] [IGVCommandBar.java:165]  Selecting genome hg38
INFO [2021-06-30 11:31:03,572] [MessageUtils.java:74]  ERROR: Could not locate genome: hg38
INFO [2021-06-30 11:31:05,573] [CommandExecutor.java:235]  ERROR: Could not locate genome: hg38
INFO [2021-06-30 11:31:05,574] [BatchRunner.java:72]  Executing Command: snapshotDirectory

/home/urangasw/Softwares/IGV-snapshot-automator-master/analysis_3 INFO [2021-06-30 11:31:07,576] [CommandExecutor.java:235] OK

The final snapshots are done using hg19 since hg38 was not located. My question here is, is the IGV version of hg38 genome available for download? If so, where? If not, what's the alternative?

1. How to change the track color of the coverage in IGV while using batch script? Suppose I have 4 cases and 4 controls, I want the coverage of cases to be red and controls to be blue. I know there is the colorby option as one of the batch command, but little is given about how to use it effectively.

I'll be glad if somebody can help me out with these problems. Have a lovely day.

Cheers, Uday

[GenoMax]

If you open IGV (graphical interface) then you should be able to select GRCh38/hg38 from the genome downloads. That should download necessary files for hg38 and cache them. There may be a way to do this on the command line but above should work.

You appear to be using an old version of IGV (3 yr?). You may want to upgrade.

[bioinfo456]

Thanks GenoMax :)

I copied the hg38.genome file that came with IGV when installed in my workstation to the genome folder of IGV on the server and it worked.

Any idea about how one could change the color of the track coverage?

[GenoMax]

http://software.broadinstitute.org/software/igv/ChangeDataDisplay#TrackColor

You may be able to use: Automatic IGV snapshot script

[bioinfo456]

I did use Automatic IGV snapshot script but I didn't find any information on how one could write a batch script to automate IGV snapshot to get a plot something like this :