If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Google Dataproc - Spark cluster service
Dataproc is Google's Spark cluster service, which you can use to run GATK tools that are Spark-enabled very quickly and efficiently. To use it, you need a Google login and billing account, as well as the
gcloud command-line utility, ak.a. Google Cloud SDK.
There are two ways to create and control a Spark cluster on Dataproc: through a form in Google's web-based console, or directly through
gcloud. Using the form is easier because it shows you all the possible options for configuring your cluster, but
gcloud is faster when you already know what you want, and you can automate it through a script. See this tutorial for details.
Once you have created your cluster on Dataproc, all you need to do to run GATK Spark tools on it is add a few arguments to your GATK command-line to tell GATK where to find your cluster. Note that your data will need to be located in Google Cloud Storage (GCS), and your file paths will need to be prefixed
gs:// accordingly. And be sure to look into jar caching to speed up the process!