Hi Galaxy-dev,
A small point of clarification to follow up on this exchange: http://gmod.827538.n3.nabble.com/GATK-v2-x-td4024851.html
In this exchange, JT mentions "those [tools] which remain under the open source license (basically, GATK 1.6)".
I assume he means GATK Lite, which includes the core GATK architecture, engine and all tools that were present in v1.6, all of which indeed remain completely open-source under the new license.
What I would like to clarify is that while GATK Lite is the continuation of the 1.6 development branch, it is more appropriately referred to as version number "2.x (lite)".
I realize there may be some confusion about the version numbering and what exactly is or isn't open-source now, so if you have any questions please feel free to email me directly at vdauwera@broadinstitute.org or post your question in our support forum at http://gatkforums.broadinstitute.org/
Regards, Geraldine