A small point of clarification to follow up on this exchange:
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 vdauw...@broadinstitute.org
or post your question in our support forum at
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