Running IGV from a batch file

[Lena Smith]

Hello,

I would like to execute a batch file from Windows command line that would start an IGV session, load bam files and tracks listed in the file.

Here is the file:

new

snapshotDirectory H:/SnapShot

load H:/test.bam

goto chr5:10000

collapse

snapshot

new

I try to execute by typing the name of the bat file in the command prompt but I get "Snapshot directory is not recognized as an internal or external command" and so on.

What is the proper way to construct and execute such a file?

Thanks,

Lena

[James Robinson]

Hi, this is not a windows batch file, it is an igv batch file.    If you want to run from the command line see http://software.broadinstitute.org/software/igv/startingIGV

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