Overhauled MuTect2 workflow #2
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This repo should also probably be renamed "MuTect2_TOOL" for consistency with naming conventions. I don't know who even owns this repo -- it looks sleepy |
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Updated the workflow to use modern wolF design patterns.
Large and complicated tasks have been decomposed into simpler tasks that form a thin wrapper around the GATK command line tools. These tasks could in principle be used to build other GATK-based workflows.
Reference build and WGS/WES are parameterized.
Default reference files are provided, but can be overridden.
The workflow can be easily called by other workflows; for example, see the PECGS CMI characterization pipeline, which is a variant of the standard characterization pipeline with MuTect2 added to it.