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Learn GATK through workshop tutorials

By Geraldine_VdAuwera

Reap the benefits of a GATK workshop without the time and expense of an international trip

For many in our community, July heralds the much welcome summer break - whether that means vacationing, or finally getting some work done without the constant disruptions of classes and committees. But for the GATK support team, it's the height of our workshop season! Next week, we'll be in Cambridge, UK; and after that the World Tour heads South to Brazil, Costa Rica and Spain. So even as we pack up our bags, this feels like a good time to highlight how any one of you can take advantage of the workshop materials without leaving your desk (or couch, or porch, or wherever you find yourself this season).

From bootcamp to boxed lessons

Our standard workshop is a four-day intensive course on, well, everything you need to know to do variant discovery with GATK. It covers the essentials of working with high-throughput sequencing data, the tools and technologies you’ll use and how to use them, and the algorithms and methods at the heart of the GATK Best Practices. The main goal is to equip participants with actionable skills and know-how, so we alternate between lectures on the theory and hands-on exercises to keep people engaged and focused on making those connections.

Starting this year, we’re basing all the hands-on sections on interactive Jupyter notebooks in our cloud platform, Terra. This liberates us from the technical friction we used to face when we had people run on their own laptops, and allows us to really focus on the data analysis instead of spending time installing apps or troubleshooting various operating systems. It also means that it's now trivially easy for us to share materials with everyone beyond the workshop cohort in a way that works right out of the box. I wrote a bit about this last week when I announced that all our new tutorials will be Jupyter notebooks.

Do it yourself

We realize that the overwhelming majority of you can't make it to a workshop in person, and that's why I find it especially exciting that we can now provide fully-loaded workspaces on Terra. With those, you can work through all the GATK workshop tutorials (see full list of links at the bottom of this post) at home or at work -- or on the beach, if you're the type who can't let go (no judgment, I'm that type). Check out my previous blog post for a walkthrough of an abridged version of a workshop tutorial so you can decide if it's the sort of thing you'd like to try out. We cover a lot of ground in the workshop tutorials, and this is a really great resource to try at your own pace -- whether you're just getting started or you're well-versed in the classic tools and looking for a primer on the newer material. You can ask us questions on the forum if you get stuck at any point. It may not be the full workshop experience, but I'm confident it will help you move forward in your work.

Workshop resources roundup

We share the slide decks from all the lectures, and for some workshops we have recordings posted on YouTube. The latest batch is slated for publication really soon, so watch the blog for an announcement -- and remember you can subscribe to email notifications for both the blog and the forum (eg to get an email when we answer your questions).

So here's a list of all the resources we provide for this. Keep in mind this is a snapshot in time, as we make updates and improvements for every new workshop, so if you read this later than say, mid-August, make sure to check that you're looking at the most recent versions.


Includes slides and workshop tutorial bundles, GATK-related posters, and links to YouTube videos


Pipelining (July 2019)
Germline variant calling (July 2019)
Somatic variant calling (July 2019)
BigQuery (July 2019)

Terra Resources

All showcase workspaces
Getting Started in Terra
Doing Research in Terra
Terra forum

And as always, the GATK forum!