https://github.com/getwilds/ww-vc-trio
Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
https://github.com/getwilds/ww-vc-trio
wdl-workflow wilds-wdl
Last synced: 5 months ago
JSON representation
Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
- Host: GitHub
- URL: https://github.com/getwilds/ww-vc-trio
- Owner: getwilds
- License: mit
- Created: 2024-04-08T22:19:39.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-08T05:18:43.000Z (about 2 years ago)
- Last Synced: 2025-10-25T22:11:11.178Z (9 months ago)
- Topics: wdl-workflow, wilds-wdl
- Language: WDL
- Homepage:
- Size: 26.4 KB
- Stars: 0
- Watchers: 0
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
> [!WARNING]
> **This repository has been archived as of 2026-01-12.** The functionality has been migrated and expanded upon in the [WILDS WDL Library](https://github.com/getwilds/wilds-wdl-library) as the [`ww-leukemia` pipeline](https://github.com/getwilds/wilds-wdl-library/tree/main/pipelines/ww-leukemia). Please refer to that instance for the latest versions, documentation, and updates.
# ww-vc-trio
[](https://getwilds.org/badges/#experimental)
This WILDS WDL workflow takes samples through a standard alignment protocol and identifies variants using a trio of well-established variant callers. Finally, the workflow narrows it down to variants of confidence by analyzing consensus amongst the three variant callers.
## Usage
For Fred Hutch users that are new to WDL, we recommend using [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this workflow directly to the on-premise HPC cluster, as it simplifies interaction with Cromwell and provides a user-friendly front-end for job submission and tracking. For users outside of Fred Hutch or more advanced users who would like to run the workflow locally, command line execution is relatively straightforward:
```
java -jar cromwell-86.jar run ww-vc-trio.wdl \
--inputs ww-vc-trio-inputs.json \
--options ww-vc-trio-options.json
```
Although Cromwell is demonstrated here, this pipeline is not specific to Cromwell and can be run using whichever WDL execution method you prefer ([miniwdl](https://github.com/chanzuckerberg/miniwdl), [Terra](https://terra.bio/), [HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html), etc.).
## Support
For questions, bugs, and/or feature requests, reach out to the Fred Hutch Data Science Lab (DaSL) at wilds@fredhutch.org, or open an issue on our [issue tracker](https://github.com/getwilds/ww-vc-trio/issues).
## Contributing
If you would like to contribute to this WILDS WDL workflow, see our [contribution guidelines](.github/CONTRIBUTING.md) as well out our [WILDS Contributor Guide](https://getwilds.org/guide/) for more details.
## License
Distributed under the MIT License. See `LICENSE` for details.