GATK4 MuTect2 workflow (beta)

This is the initial release of the GATK4 MuTect2 workflow for somatic SNV and Indel discovery developed by the GATK team at the Broad Institute. It includes the core workflow WDL, a JSON of inputs for the exome use case, and a JSON of generic options for running via Cromwell on the Google Pipelines API (PAPI).

Requirements

The workflow was tested with GATK version 4.beta.3 and is expected to work with versions up to 4.beta.5 (current version at time of release). It should be runnable on any platform that supports WDL. The included JSON points to data files hosted on the Google Cloud Storage platform.