https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels

Last synced: 3 days ago
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Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

• Host: GitHub
• URL: https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels
• Owner: gatk-workflows
• License: bsd-3-clause
• Created: 2019-08-27T18:23:33.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2021-09-13T11:18:44.000Z (over 3 years ago)
• Last Synced: 2023-03-01T04:01:11.033Z (almost 2 years ago)
• Language: wdl
• Size: 38.1 KB
• Stars: 45
• Watchers: 4
• Forks: 33
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome_ai_agents - Gatk4-Rnaseq-Germline-Snps-Indels - Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools (Building / Workflows)
• awesome_ai_agents - Gatk4-Rnaseq-Germline-Snps-Indels - Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools (Building / Workflows)

README

        
# gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

### Requirements/expectations :

 - uBAM 

### Output :

 - A BAM file and its index.

 - A VCF file and its index. 

 - A Filtered VCF file and its index. 

 Runtime parameters are optimized for Broad's Google Cloud Platform implementation.

 For program versions, see docker containers.

### Important Notes :

- Runtime parameters are optimized for Broad's Google Cloud Platform implementation.

- The provided JSON is a ready to use example JSON template of the workflow. Users are responsible for reviewing the [GATK Tool and Tutorial Documentations](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) to properly set the reference and resource variables. 

- For help running workflows on the Google Cloud Platform or locally please

view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).

- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360035890811).

### Contact Us :

- The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : [GATK](https://gatk.broadinstitute.org/hc/en-us/community/topics) or [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432).

### LICENSING :

 This script is released under the WDL source code license (BSD-3) (see LICENSE in

 https://github.com/broadinstitute/wdl). 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. Please see the docker

 page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed

 licensing information pertaining to the included programs.