This repository contains Jupyter Notebooks that walks users through GATK Best Practices Workflows.

• Day2
  • 1-gatk-germline-variant-discovery-tutorial.ipynb
  • 2-gatk-hard-filtering-tutorial-python.ipynb
  • 3-gatk-hard-filtering-tutorial-r-plotting.ipynb
  • 4-gatk-cnn-tutorial-python.ipynb
• Day3
  • 1-somatic-mutect2-tutorial.ipynb
  • 2-somatic-cna-tutorial.ipynb

• GATK 4.1

• If you are executing these notebooks on Terra workspace, be sure to use the following startup script when creating a cluster: gs://gatk-tutorials/scripts/install_gatk_4100_with_condaenv.sh
• Relevant reference and resources bundles can be accessed in gs://gatk-tutorials/workshop_1903.
• The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : GATK , FireCloud or Terra , WDL/Cromwell.
• Please visit the User Guide site for further documentation on our workflows and tools.

Copyright Broad Institute, 2019 | BSD-3 This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.