running IGV from command line

[epi]

I am running the following commands:

java -Xmx750m -jar igv.jar
works!

java -Xmx750m -jar igv.jar -g mm9
works!

java -Xmx750m -jar igv.jar -g mm9 -b test.bam
prints gibberish on command line........ wht happened??

Please respond how can I load bam file form command.

p.s. Same bam file works from GUI

[Jacob Silterra]

The "-b" flag is for an igv batch script. You can find details on
creating those here:
http://www.broadinstitute.org/software/igv/batch

If the only thing you want to do is open a file, no flag is used.

Just enter:

java -Xmx750m -jar igv.jar -g mm9 test.bam

-Jacob

--
Jacob Silterra
Software Engineer
Broad Institute