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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@geoffjentry @PatriciaMBrent Indel realn gone now; much faster BQSR + Sparkified tools in GATK4a. And wider scope of application/ use cases.
9 Dec 16
@geoffjentry @PatriciaMBrent B fair, other slide says results similar. Not uncommon for benchmark tests. But speed comparison v outdated 1/2
9 Dec 16
RT @geoffjentry: Talk by Stavros Papadopoulos about TileDB from @intel - used by @BroadGenomics to power our joint genotyping https://t.co/
8 Dec 16
@iskander @NJL_NGS Hm. Can you please post this in the forum?
8 Dec 16
@iskander @NJL_NGS Treat them like any other read, no special handling. Problems arise in CIGAR functions that don’t know how to handle Ns.
7 Dec 16

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