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 Google Cloud
At this time we are able to offer two services for running WDL workflows on Google Cloud using the Cromwell execution engine and the Google Pipelines API. Note that while access to both of these services is free, compute and storage are subject to Google Cloud pricing, charged directly by Google (Broad does not apply any markup).
Terra: Our secure, freely accessible cloud-based analysis portal
This web-based application is provided as a freely accessible service by the Broad Institute's Data Sciences Platform, where GATK itself is also developed. Terra (formerly FireCloud) provides both GUI (point-and-click) and API access to a persistent Cromwell execution server that manages submissions to the Google Pipelines API. In addition to the core pipeline execution service, the Terra platform also includes functionality for data management, a data library of published datasets (including TCGA data) and a method repository for managing and sharing workflows. The platform as a whole is designed to empower analysts, tool developers and production managers to perform large-scale analysis, engage in data curation, and store or publish results. You can find out more about how Terra can make it easier for you to run GATK Best Practices pipelines here.
Google Pipelines API + WDL_Runner
These open-source command-line utilities were developed by Google Cloud to enable execution of analysis pipelines on the Google Cloud platform. The Google Pipelines API is a pipeline execution service that runs jobs on the Google Compute Engine (GCE). WDL_Runner is a package that provides support for running workflows written in WDL through the Pipelines API, via a Cromwell server that is spun up and torn down ad-hoc by WDL_Runner itself. See the GATK on Google Genomics tutorial for a hands-on demonstration of how to run one of our Best Practices production workflows on this service.