There are many ways to run GATK for your analyses, and the best option for you depending on what infrastructures you are most comfortable working with.
Terra, the user-friendly choice
Our first recommendation for researchers using GATK is Terra. Developed by the Broad Institute's Data Sciences Platform (where GATK itself is developed), Terra provides a user-friendly graphical interface for setting up, running, and sharing your pipelines using Jupyter notebooks. More information is available at the link below.
- GATK on the cloud with Terra - It's easier to collaborate and publish data, figures, and workflows without needing to manipulate any underlying computational infrastructure.
GATK on other computing platforms
If you're the kind of person who is comfortable working directly with cloud infrastructure, then GATK is able to work on whichever system you are most familiar with.
Alibaba Cloud - China's largest cloud provider has utilities that leverage Cromwell to execute analysis pipelines.
Amazon Web Services - We are adding support for running Cromwell on AWS Batch and integrating with AWS products.
Google Cloud - The Cromwell execution engine and the Google Pipelines API can be used for running WDL workflows on Google Cloud.
Local HPC infrastructure - Intel provides a fully integrated solution to help users set up and run GATK workflows on HPC.
GATK with WDL and Cromwell
We aim to provide the research community with a range of options for running our Best Practices workflows exactly the same way we do it in-house at the Broad Institute. To that end, we make all our workflow scripts available publicly, so you can use and edit the scripts for your own research.
- Pipelining GATK with WDL and Cromwell - Our workflows are written in WDL, a user-friendly scripting language maintained by the OpenWDL community.