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This is one of two posts announcing the imminent beta release of GATK4; for a technical description of features, see this other post.

"Wait, what?" Yes, you read that right, we're moving GATK4 to a fully open source license -- specifically, BSD 3-clause. And to be clear, this applies to all of GATK4. Not just the core framework (which, little known fact, has always been open source), but all the tools that were previously "protected", including HaplotypeCaller, the new CNV discovery tools, everything. The whole enchilada.


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Unboxing GATK4

Posted by Geraldine_VdAuwera on 24 May 2017 (0)


This is one of two posts announcing the imminent beta release of GATK4; for details about the open-source licensing, see this other post.

You've probably heard it by now: we are on the cusp of releasing GATK4 into beta status (targeting mid-June), and we plan to push out a general release shortly thereafter (targeting midsummer). That's great. So what's in the box?

Over two years of active development have gone into producing GATK4, and I'm happy to say we have plenty to show for it. Specifically, we've pushed the evolution of GATK on three fronts: (1) technical performance, i.e. speed and scalability; (2) new functionality and expanded scope of analysis, e.g. we can do CNVs now; and (3) openness to collaboration, through [open-sourcing](link to BSD blog post) as well as general developer-friendliness (documented code! consistent APIs! clear contribution guidelines!).

Want more detail? Let me give you a tour of the highlights, using slides from the presentation I gave at Bio-IT earlier today (code reuse: it's not just for code anymore).


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This is becoming a bit of a yearly tradition; next week we're heading over to Bio-IT World Expo in Boston (so a short hop across the Charles River) to announce the majorly rebooted version of GATK which we've affectionately dubbed GATK4. Because it will be version 4.

Look, if you've ever seen the names we give our tools, you know that naming things isn't exactly where we put our creativity to work. It's a precious resource, and anyway we rather like things to be self-explanatory.

Yes, technically we already announced GATK4 at Bio-IT last year, but no, this is not a re-run. Last year was a heads-up that we were working on this significant new reimplementation of the toolkit. We were mostly there to talk about the core features of the new framework, which famously excited the Spark-savvy in the crowd (because it supports Apache Spark). But it was definitely still under heavy development; while we had the CNV tools just about ready for testing, as I recall there wasn't even a glimmer of the HaplotypeCaller in there yet.

This year is very different. We have a toolkit that is in the final stages of polishing up for public consumption. We have multiple Best Practices workflows, because we're not just about the germline SNPs and indels anymore. And we also have numbers. Dates for the beta and full releases, performance estimates...

All of which we'll present during a luncheon event we're holding with our wonderful partners at Intel Life Sciences, who have contributed some of GATK4's key new features. The luncheon will take place Wednesday the 24th at 12:40 PM, at a location TBD (because I can't figure it out from the Bio-IT program, which is not self-explanatory). We'll be in Track 1: Data and Storage Management, which may sound super boring (no offense to other speakers in this track) but come on and join us if you can; I predict you'll be pleasantly surprised.

As a coda, we'll be holding Q&A sessions in the Intel Hospitality Suite, aka Dartmouth room in the WTC, at the following times: Wednesday the 24th from 1:30 PM to 3:15 PM, and Thursday the 25th from 10:30 to 11:30 AM. Swing on by if you have any burning questions about GATK4.

We look forward to seeing you there! And if you can't make it because of trivial considerations like geographical incompatibility (oceans, shmoceans), check out this blog or follow @gatk_dev on Twitter. We'll post a summary of the announcements shortly after the luncheon presentation.


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As part of our job providing support to the GATK user community, our team takes turns traveling to conferences, both to learn what's going on in the field at large and to advertise the latest features of the GATK. I recently attended the Advances in Genome Biology and Technology (AGBT) general meeting in Hollywood, Florida in February. Nice time of year to go there!

When we go to conferences we often do workshops or present posters, but this time was a first: I was there to do a software demo. Well, in fact I had two demos prepared: one about using GATK4 to run commands directly on a Spark cluster, and the other about running GATK workflows on the Cloud using Google's Pipelines API.


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What is beagle.

Beagle is a type of dog known for its even temper and intelligence. It is also the name given to the ship Darwin sailed to the Galapagos (the H.M.S. Beagle), where he developed his theory of natural selection from observing finches. It is also the name of a genomics software package known for phasing and imputing genotypes. Beagle also calls genotypes and detects identity-by-descent (IBD), i.e. it can find segments of identical DNA that indicate two individuals are related.

I will be writing a series of posts where I share with you how I take 23andMe raw data to locate IBD segments using Beagle v4.1 (website; doi:10.1534/genetics.113.150029). For a review of the statistical methods and other theory underlying IBD, see doi:10.1534/genetics.112.148825. To see a skipper’s dog on a ship at sea, watch Irving Johnson’s footage of the Peking barque.


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A few of us GATKers (among a flood of other Broadies) traveled to Washington, DC this week for the General Meeting of the American Association for Cancer Research (AACR). Here are PDF copies of the posters we presented on Tuesday morning.

Abbreviated title Presenter Link
Somatic mutation discovery with GATK4 Geraldine Van der Auwera PDF
Allelic Copy Number Variation Discovery Aaron Chevalier PDF
Copy Number Variation Discovery in WGS and Exomes Mehrtash Babadi PDF

Incidentally, it's the end of the conference so now 10,000 people are trying to get home, and apparently half of them are going to Boston. I was hoping to catch an earlier flight on standby; the gate attendant laughed so hard. Most of the flights are overbooked to start with. So I have some time to kill until 9 PM. Well, I guess there's plenty of documentation in need of writing!

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You may have heard that we've been working on a major new release of GATK that we call GATK4. As we are getting closer to the scheduled transition of GATK4 into beta status (from its current lowly alpha state), we are putting a lot work into fine-tuning the user-facing aspects of the program. We realize that many of our users struggle to make sense of the variety of tools and their numerous options and parameters, and that when something goes wrong, the error messages can seem cryptic and/or overwhelming.

So one of the things we're experimenting with is an interactive support feature that you can invoke directly from the command line, and that should help you figure out solutions to most problems that you might encounter while using GATK. It's not quite fully-featured yet but we'd like to get some feedback to evaluate whether it is helpful to real users, and determine how we can further improve it.

You can download a precompiled jar (fully open source under a BSD license) where this feature is enabled by default, from this page: https://software.broadinstitute.org/gatk/download/gatk4_1. The command syntax is essentially the same as for the current version of GATK, except you no longer provide -T to specify the tool, and -o is all grown up and is now -O. You can get usage information for any tool by doing e.g. java -jar GenomeAnalysisTk-4_1.jar PrintReads -h the same way as you would with the current GATK.

Please try it out and let us know what you think!

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Here are some rules-of-thumb for posting questions

  1. Post a new question instead of continuing an ongoing discussion thread. The exception to this is if your question relates directly to the discussion thread, i.e. comments on the original post or answers a question asked in the thread. To refer to a particular thread, you can include its URL.

  2. Post the question once. This is the case even if you post to the wrong subforum. We can easily move your post to the appropriate one.

  3. Questions relate to running a GATK tool, Picard tool, GATK Best Practice Workflow, WDL script, Cromwell or FireCloud. All other questions, e.g. those about non-GATK tools, you should ask the Biostars or SeqAnswers forums.

Next, I point out specific guidelines for GATK questions, give a formatting tip and explain the motivation behind this note using pie.


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These are the materials that we are presenting at the February 2017 GATK workshop in Leuven, Belgium.

Materials Link
DAY 1: GATK Best Practices talks
Slide decks presented on Day 1 Google Drive Folder
DAY 2: Germline variant discovery
Variant Discovery Tutorial Worksheet (Day 2 AM) PDF on Google Drive
Variant Filtering Tutorial Worksheet (Day 2 PM) PDF on Google Drive
Germline Data Bundle (Day 2) ZIP on Google Drive
DAY 3 AM: Somatic mutation discovery
MuTect2 Tutorial Worksheet (Day 3 AM) PDF on Google Drive
MuTect2 Data Bundle (Day 2) TAR.GZ on Google Drive
CNV Tutorial Worksheet (Day 3 AM) PDF on Google Drive
CNV Data Bundle (Day 3 AM) ZIP on GATK website
DAY 3 PM: Pipelining with WDL
WDL Pipelining Tutorial Worksheet (Day 3 PM) PDF on Google Drive
WDL Pipelining Data Bundle (Day 2) ZIP on Google Drive
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I want to give mad props to my team. Every day they handle new questions about obscure error messages or unusual experimental designs, on top of their ongoing efforts to develop new documentation materials and keep up with the latest innovations that the dev team is working on. All of this in service of a community with a very wide range of use cases -- and levels of comfort with the biology and/or computational aspects of genomics. It's a challenging job, especially when the tools and technology keep evolving under your feet, and the science itself refuses to stop mutating. Poetic, I suppose, if inconvenient.

And that's why we are a team with a wide range of strengths, backgrounds and interests as you can see in the 2017 team roster below.

So, please say hello in the comments if you appreciate this team's efforts, or really make our day and send us a postcard! One online commenter and one postcard sender will each be chosen at random* and receive a GATK-themed prize**.

Our mailing address is:

GATK Outreach, c/o G. Van der Auwera
Broad Institute, Room 415M-7100-B
415 Main Street,
Cambridge MA 02142
USA

* We reserve the right to implement random selection at our discretion. I expect it will be a low-tech implementation involving printing out bits of paper, folding them and having a random grad student in the cafeteria pick one out of a hat.

** Nature of prizes also to be determined as I need to find out how much of my outreach budget I can use for this. I can pretty much guarantee that the prizes will have no real monetary value, but will come with serious bragging rights.


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GATK Dev Team

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RT @broadinstitute: Upcoming release of #GATK4 will bring significant speed optimization, new tools, and open source licensing https://t.co
25 May 17
Delighted to confirm that as of today we are open-sourcing #GATK under BSD 3-clause. https://t.co/EexX6emSkP
24 May 17
RT @BroadGenomics: Missed the GATK4 presentation? Ask your questions about open sourcing & GATK4 at @IntelHealth suite (Dartmouth Room) wit…
24 May 17
Join us at #BioIT17 for lunch with Intel, big GATK4 news and Q&A sessions https://t.co/AK1ttbFVV5 https://t.co/ynWTnmce4T
24 May 17
RT @broadinstitute: Broad will be busy at #BioIT17. Check out the presentations, demos, and Q&A sessions on this year’s schedule: https://t…
24 May 17

Our favorite tweets from others

best error output: Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
4 Apr 17
From the @gatk_dev page describing .vcf files: "Don't write home-brewed VCF parsing scripts. It never ends well” https://t.co/28KcRoV14j
28 Feb 17
Our 3-day course on GATK https://t.co/mtN60KRTyS finished - 38 participants very happy! Big thanks to @gatk_dev team for excellent lessons.
24 Feb 17
@froggleston @dgmacarthur Sounds like ExAC is reaching Uber stage. ‘Uber but for pizza’. ‘ExAC but for wheat’.
14 Jan 17
#ESRenpeinture grad school - postdoc - after postdoc https://t.co/o3vQMgBDgk
6 Jan 17
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