IGV batch scripts



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

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.




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