We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GATK on the cloud with Terra (previously FireCloud)
Terra is an open platform for secure and scalable analysis on the cloud.
More concretely, it's a web-based portal that is provided as a freely accessible service by the Broad Institute's Data Sciences Platform, where GATK itself is also developed. Terra is designed to make it easier to share and access large datasets, run analyses at any scale and work collaboratively across groups and organizations without having to worry about the underlying computational infrastructure. Current functionality includes a growing library of datasets, a Cromwell server for pipelining and Jupyter Notebooks for interactive analysis.
You can read more about how and why you can get started with GATK in Terra in this series of blog posts:
- Getting started with GATK? Terra can make it easier
- Test drive GATK Best Practices workflows on Terra
- The future of GATK tutorials is written in Jupyter Notebooks
- From Python Magic to embedded IGV: A closer look at GATK tutorial notebooks
- Learn GATK through workshop tutorials
All the Best Practices workflows, ready to run
As part of our effort to make it easier for everyone to try out GATK regardless of their personal level of (dis)comfort with the intricacies of computational infrastructure, we make all of our Best Practices workflows (plus various additional utilities) available in Terra. This takes the form of workspaces where the workflows are preconfigured for common use cases, along with example data that is suitable for testing and benchmarking, both at small scale and at full scale. So it should just be a matter of a few clicks to run any pipeline you like on the preloaded example datasets -- or, with a few more (simple) steps, to run them on your own data. All this without ever touching a command line, unless you're the CLI-over-GUI type, in which case you're welcome to use the Terra FireCloud APIs vis Swagger or the FISS Python bindings to do all this programmatically.
We hope this will enable researchers to spend less time figuring out how to run GATK Best Practices and more time doing interesting science with the results. We also believe this will boost portability and reproducibility in genomic analysis.
Free Credits Program
We understand that moving your analysis to the cloud is a big cultural and logistical shift, and there is a clear need to make it possible to try out such a new option without having to commit financially. To address that need, we've teamed up with Google Cloud to give away free credits for trying out Terra. Learn more about this free credits program in the Terra Free Credits documentation.