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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.
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.
Most of the queue.extensions are generated classes once you run 'ant'. The generated classes are Queue compatible versions of the walker command arguments. Instead of looking at the generated scala file you can find the same or better argument descriptions in the the gatkdocs for each walker.
The 'incomplete' status of the script means that it is only a technical example, and will need to be tweaked for your specific requirements in your calling pipeline. Feel free to explore different command line options with the UG. For example using Queue you can create two instances of the UG and test using with BAQ and without. As for what UG commands you should be using, see the UG gatkdocs and the Best Practices for an overall description of where the UG fits in a calling pipeline.
Thank you! That cleared things up for me.