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One more 3.x version, for the road! That's right, even as we're ramping up our efforts on GATK4 (we're three beta releases in at this point, and getting down to brass tacks writing the migration guide ahead of the 4.0 general release) we still found it worthwhile to cut one last release of GATK3.

Our main motivation here is to introduce the Intel Genomics Kernel Library, which comes bearing the gift of speed improvements for those of you who won't be able to migrate to GATK4 right away.

As a secondary benefit, this version includes a handful of bug fixes, some usability improvements including better error messages, documentation fixes and logging tweaks, and a few improvements to annotation calculations (especially in allele-specific mode), which you'll find described briefly in the release notes. No big changes though, except perhaps the new default behavior of VariantsToTable with regard to missing annotation values, discussed below. Finally, we've committed a copy of all the peripheral documentation (= the docs that live in the forum and complement the tool documentation) to the now-old GATK codebase.

And thus, the last-ever GATK3 version emerges covered in carbonite.

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GATK 3.8 was released on July 28, 2017. Itemized changes are listed below. For more information on what you should care about, see the user-friendly version highlights.

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Today we are reaching out to the Chinese research community with great news: we are partnering with key companies and institutions in China to empower Chinese researchers to use GATK effectively and at scale.

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We've been getting so caught up in the excitement of the imminent beta release of GATK4 (possibly later this week!), we forgot to announce upcoming workshops! And two of them are coming up fast, in just a month from now. Specifically, we'll be in Cambridge, UK, July 12-14 and then in Edinburgh, UK, July 17-19. There's still time to register for both but the hands-on sessions have limited space, so don't wait around!

GATK is also going to be making a brief appearance at BOSC '17 in Prague, CZ, July 21-22. Our team member Kate Voss will give a lightning talk and present a poster about our genomics pipelining stack that is composed of GATK4+WDL+Cromwell. I'm frankly delighted that our abstract was accepted as a late-breaking submission; it's a pleasure to kick off the new open-source era of GATK at the most open-sourcey meeting of the year!

Going forward, be sure to check out the new Events calendar feature we just now added to the website to help you keep track of events more systematically.

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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 (5)

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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GATK Dev Team


I added a video to a @YouTube playlist 2017-07-23 Kate Voss "Full stack genomics pipelining with GATK4 + WDL +
6 Aug 17
RT @IntelHealth: Learn about the Genomics Kernel Library (GKL), which helps developers accelerate #genomics applications.
3 Aug 17
RT @dgmacarthur: Work with my team to help change the lives of rare disease patients. Software engineering and compbio roles open: https://…
1 Aug 17
@CuiJack No sorry, GGA mode is not yet supported in GATK4 HaplotypeCaller.
1 Aug 17
I added a video to a @YouTube playlist Broad Institute — GATK in the Cloud: Running genomics pipelines at
29 Jul 17

- Our favorite tweets from others

Round of applause at #BOSC2017 for GATK4 being open sourced.
23 Jul 17
Round of applause for @Katewanders - Broad Institute will open source data science tools from now on #BOSC2017
23 Jul 17
The @gatk_dev team, that delivered an excellent "GATK Best Practices for Variant Discovery" workshop this week, on…
20 Jul 17
Amazing session @edgenome with @gatk_dev comes to an end. Enriched learning! Thx #gatk #gatk2017 #Genomics #Edinburgh #Bioinformatics
19 Jul 17
Great day of lectures on GATK Best Practices yesterday. Very clear and useful. Thanks! @gatk_dev @edgenome
18 Jul 17
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