Dear Community,

After careful consideration, we have decided to shift our focus to new and innovative initiatives that will better serve our community and align with our long-term goals.

Effective Date: May 12th, 2025

Impact on Users:

• The project repository will be archived and set to read-only mode, ensuring that it remains accessible for reference.
• While no further updates, bug fixes, or support will be provided, we encourage you to explore the wealth of knowledge and resources available in the repository.
• Existing issues and pull requests will be closed, but we invite you to engage with other projects and contribute your expertise.

Licensing: The project will remain under its current open-source license, allowing others to fork and continue development if they choose.

We understand that this change may come as a surprise, but we are incredibly grateful for your support and contributions over the years. Your dedication has been instrumental in the success of this project, and we look forward to your continued involvement in our future endeavors.

Thank you for your understanding and support.

Short variant discovery in RNAseq data on Azure

This repository is an example of running the RNAseq short variant discovery pipeline, based on Best Practices RNAseq Short Variant Discovery Pipeline by Broad Institute of MIT and Harvard, on Cromwell on Azure.

Learn more about using Azure for your Cromwell WDL workflows on our GitHub repo! - Cromwell on Azure.

This repository is a fork from the original and has all the required changes to run the WDL workflow on Cromwell on Azure.

Here, you can find the WDL file and an example inputs JSON file with links to data hosted on a public Azure Storage account. You can use the "datasettestinputs" storage account directly as a relative path, like in the inputs JSON file.

The gatk4-rna-germline-variant-calling.trigger.json trigger file is ready to use. You can start the workflow on your instance of Cromwell on Azure, using these instructions.

gatk4-rnaseq-germline-snps-indels

Purpose :

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.

Software version :

For program versions, see docker containers.

Important Notes :

• The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables.
• 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 or Terra.

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.