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.
Workshop season is right around the corner
We recently rolled out a fresh new edition of our popular 4-day GATK bootcamp, which we trialed at the Broad, and now we're excited to take it on the road! We have six locations lined up, one every month for the next six months. We're going to be bouncing around Europe quite a bit, with a couple of side trips to Central and South America:
- May 14-17: Helsinki, Finland (register here)
- June 18-21: Newcastle, UK (register here)
- July 8-11: Cambridge, UK (register here)
- August 26-29: São Paulo, Brazil
- October 21-24: Seville, Spain
(registration links will be added as they become available)
In this bootcamp-style workshop, we take you through the basics of working with genomic sequence data and a high-level overview of variant discovery so that by the end of the first day, you have a solid understanding of all the main pieces and processes. Then over the course of the next two days we delve into the details of variant calling for the most mature supported use cases -- germline SNPs and Indels on Day 2, somatic SNPs and Indels and somatic copy number (CNVs) on Day 3 -- through a combination of lectures and hands-on tutorials. Finally, on the fourth day we cover the mechanics of assembling and executing analysis workflows, as well as some useful tools and newer use cases that are hot off the development press.
The most innovative feature of this season is that we'll be running all hands-on tutorials on the Broad's new cloud-based analysis platform, Terra (the next-gen version of FireCloud), which you can learn more about at https://terra.bio. Terra is currently in a closed beta phase until May 1st, but you can already request access by filling in a contact form at https://terra.bio/contact. Going forward Terra will be our primary channel for delivering tutorials, working examples of GATK-based analyses and more, so be sure to check it out even if you don't plan to move your work to the cloud.