running GATK Queue script under PBS environment?

[orionzhou]

Hi, I am wondering if any of you have the experience running the GATK Queue scripts (for parallelism) under PBS environment.

It seems the Queue.jar only accepts -bsub command:

http://www.broadinstitute.org/gsa/wi...the_first_time

[severin]

PBS Torque

Did you ever figure his out? I find the GATK-Queue documentation a little lacking for applying to individual systems. The Best practices document appears to have pieces of code that correspond to each of the steps but not the base script that you put those pieces into.