gatk4-jupyter-notebook-tutorials

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gatk4-jupyter-notebook-tutorials

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This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

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# gatk4-jupyter-notebook-tutorials

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

### Notebooks :
- 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
  
### Software version notes :
- GATK 4.1
  
### Important Note :
- 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](https://storage.googleapis.com/gatk-tutorials/scripts/install_gatk_4100_with_condaenv.sh)
- Relevant reference and resources bundles can be accessed in [gs://gatk-tutorials/workshop_1903](https://console.cloud.google.com/storage/browser/gatk-tutorials/workshop_1903/?project=broad-dsde-outreach&organizationId=548622027621).
- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [FireCloud](https://gatkforums.broadinstitute.org/firecloud/categories/ask-the-firecloud-team) or [Terra](https://broadinstitute.zendesk.com/hc/en-us/community/topics/360000500432-General-Discussion) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
- Please visit the [User Guide](https://software.broadinstitute.org/gatk/documentation/) site for further documentation on our workflows and tools.

### LICENSING :
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.

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