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IGV use --name command line option in a batch file

Hi,

I can load a CRAM file from the command line while renaming the track on the fly, like so:

igv --genome my_genome --name my_track my_cram.cram

my_genome is a custom built genome file that takes quite a while to load. I'd like to run an IGV batchfile for ~100 samples, and starting igv for each of them is a waste of time. I'd like to start IGV once, load the genome and then load and unload the CRAMs as required. However, I'm unable to find a batch command that lets me rename the track after I load the file.

Does anyone know how I can load a data file and have the track be named something else? Can I load track_name=data_file or something like that?

igv
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written by Ram Ram

1 answer

I guess I really should have tried harder before asking here. Much like the index= parameter described here, I can simply add a name= in the load command like so:

load /path/to/my_cram.cram name=my_track
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written by Ram Ram

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