gatk4-jupyter-notebook-tutorials

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

gatk4-jupyter-notebook-tutorials

★ 26 Open GitHub ↗

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# 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.

gatk4-jupyter-notebook-tutorials

Explore Similar Repositories

Was this content helpful?

Recent Feedback

Download README