Yep, you read that right, the next release of GATK is going to be the big Three-Oh!

You may have noticed that the 2.8 release was really slim. We explained in the release notes, perhaps a tad defensively, that it was because we’d been working on some ambitious new features that just weren’t ready for prime time. And that was true. Now we’ve got a couple of shiny new toys to show for it that we think you’re really going to like.

But GATK 3.0 is not really about the new features (otherwise we’d just call it 2.9). It’s about a shift in the way we approach the problems that we want to solve -- and to some extent, a shift in the scope of problems we choose to tackle.

We’ll explain what this entails in much more detail in a series of blog posts over the next few days, but let me reassure you right now on one very important point: there is nothing in the upcoming release that will disrupt your existing workflows. What it will do is offer you new paths for discovery that we believe will empower research on a scale that has previously not been possible.

And lest you think this is all just vaporware, here’s a sample of what we have in hand right now: variant calling on RNA-Seq, and a multisample variant discovery workflow liberated from the shackles of time and scaling issues.

Stay tuned for details!


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@BrianPardy Great, thanks for the feedback!
28 Sep 16
@BrianPardy Thank you! Does anything in particular stand out? We'd love to know what people find most useful so we can do more of the same.
28 Sep 16
#GATK workshop crew is in Basel, ready to roll! @ISBSIB https://t.co/m56JzpC1bN
25 Sep 16
@thatdnaguy That's right, we've retired it, see https://t.co/epbvwOQVTt
23 Sep 16
@geoffjentry @BroadGenomics Ah, you should ask @WDL_dev on the WDL forum then :)
21 Sep 16

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I've easily written my first custom ReadFilter for GATK. The @gatk_dev 's toolkit is a great example of programming.
21 Sep 16
@gatk_dev "make it so"
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it's the nightly build owl for GATK :D https://t.co/OwTRrk6KHA https://t.co/rfmAbdIIQp
11 Aug 16
We're going to make an hg38 version of ExAC. And we'll make @dgmacarthur pay for it. #BioinformaticsCampaignPromises
2 Aug 16
You’re right @gatk_dev honesty is key! About variants manual filtering: “In any case you're probably in for a world of pain.” Ha now I know!
11 Jul 16
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