We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 events update for Fall 2017: ASHG and more!
Fall is my favorite season -- it combines the best weather in New England and the most active period of the year for GATK events and announcements (although sometimes the latter means we don't get to go out and enjoy the former as much as we'd like). In keeping with that, we have a couple of important announcements that will go out early next week. However I'm breaking radio silence now to give you a quick update on what's been happening with regard to events and workshops, specifically.
Coming soonest: FLOW pipelining workshop showcasing GATK4 pipelines, organized by DNAstack in Orlando, Oct 17
Plus upcoming GATK workshops and links to recent workshop materials.
ASHG in Orlando, FL (Oct 17-21)
The yearly meeting of the American Society for Human Genetics is always a hotspot for us, so we've got a lot going on there:
- A 2-hour pipelining workshop called FLOW, organized by DNAstack, where we'll be demoing running GATK4 pipelines written in WDL. It's an evening workshop, 7-9pm on Tuesday 17; there are still a few spots left so sign up now.
- A poster presentation about GATK4's expanded scope of analysis (PgmNr 758/T, 3-4pm on Thu 19). Come visit Soo Hee Lee (support team) and Louis Bergelson (engine development team) to learn what GATK4 will enable you to do in your research!
- GATK4 demos and Q&A at the Broad Genomics booth (#1037 in the Exhibition Hall, Orange County Convention Center South Building, Floor 1), Thursday 19, 11:30-12:30 and Friday 20, 10:30-11:30. If you miss the poster presentation or you'd like to ask the kind of questions that are best answered with a running laptop, this would be your time.
- FireCloud demos and Q&A, also at the Broad Genomics booth, Wednesday 18 afternoon, all day Thursday 19, and Friday 20 morning. The demos are scheduled for 3pm on Wednesday and Thursday; the rest of the time is open for walk-up questions and 1:1 guided tours. This is a great opportunity to learn how FireCloud, our cloud-based analysis platform, can help you by taking the pain out of pipelining GATK (or anything else you want to pipeline, really).
GATK workshop in Pretoria, South Africa (Oct 23-27)
This is a "bootcamp special" version of our popular workshop series, running five entire days, with interleaved talks and hands-on exercises, hosted by the University of Pretoria. I'm not sure there are any spots left but if you're interested (and presumably, local to that part of the world, given the short time remaining), see this document.
GATK workshop in Huntington, West Virginia (Nov 8-10)
This one is our classic workshop formula, running three days with one day of talks and two days of hands-on exercises, hosted by the WV-INBRE Bioinformatics Core Facility. It's open to all comers and I believe there are still a few spots left, for which you can register here.
SuperComputing '17 in Denver, Colorado (Nov 12-17)
We'll be demoing GATK4 pipelines running on Google Cloud; exact schedule TBD.
We are currently developing the workshop schedule for 2018, and are so far talking with several prospective hosts in Europe, North America and Asia. We hope to be able to offer a good selection of locations worldwide. And we're still taking requests, so don't hesitate to reach out to us if you'd like to consider hosting us yourself!
Latest workshops materials
We held several workshops this summer; Cambridge and Edinburgh in July, and Helsinki in September. As always, the latest workshop materials (Helsinki version) are accessible from the Presentations page. If you're lazy (or should I say effort-averse), here's a direct link to the relevant Google Drive folder -- but keep in mind this will not remain the latest version for long.