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It says in the "ExampleUnifiedGenotyper" qscript that it runs an incomplete version of the UnifiedGenotyper. I have a two questions about this.
I cannot find the org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper class, is this not in the public source or am I blind?
Does the "incomplete" in the script starting comment mean that this extension is incomplete in its functionality? Or is it something else that is incomplete in its nature?
Basically I'm wondering if there are any pitfalls for me if I start using the example script as a base for my own variant calling qscript.