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!

Comment on this article in the forum

At a glance

Follow us on Twitter

GATK Dev Team


RT @BroadGenomics: Missed #GATK WKSP at #ASHG16? 10am meet Geraldine at booth 329 - Broad’s GATK Guru @gatk_dev #BroadGenomicsExperts https…
20 Oct 16
RT @NJL_NGS: Broad Institute Workbench workshop now at #ashg16.
19 Oct 16
RT @konradjk: We're rebranding a bit! gnomAD now adds WGS regions, as well as doubling the data depth and increasing diversity (5K ASJ!) #A…
19 Oct 16
RT @NJL_NGS: now launched!
19 Oct 16
RT @dgmacarthur: For those who missed it: we just posted variant frequencies from 126,216 exomes and 15,136 genomes at
19 Oct 16

Our favorite tweets from others

Asked a question, speaker jokes not to edit your BAM header and expect GATK to let you get away with it.
19 Oct 16
My new hobby: finding incomprehensible diagrams on office whiteboards and adding alarming conclusions to them
30 Sep 16
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"
8 Sep 16
it's the nightly build owl for GATK :D
11 Aug 16
See more of our favorite tweets...
Search blog by tag

ad appistry ashg ashg16 benchmarks best-practices bug bug-fixed cancer cloud cluster cnv commandline commandlinegatk community compute conferences cram cromwell denovo depthofcoverage diagnosetargets error fix forum gatk3 gatk4 genotype genotype-refinement genotypegvcfs google grch38 gvcf haploid haplotypecaller hg38 holiday hts htsjdk ibm java8 job job-offer jobs license meetings mendelianviolations multithreading mutect mutect2 ngs nt outreach pairhmm parallelism patch performance phone-home picard pipeline plans ploidy polyploid poster presentations printreads profile promote release release-notes rnaseq runtime saas script search selectvariants sequencing service slides snow speed status sting support syntax talks team terminology third-party-tools topstory trivia troll tutorial unifiedgenotyper vcf-gz version-highlights versions vqsr wdl webinar workflow workshop