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Broad Institute and Google Genomics launch GATK as a Service Jun 24

It’s an exciting week here at GATK HQ because we finally get to tell you about this very cool project we’ve been working on: today, Broad and Google announced plans to make GATK available as a service on Google Cloud Platform as part of Google Genomics!

Our goal with this project is to enable researchers around the world to run the latest version of the GATK Best Practices pipeline without the hassle of figuring out the plumbing or storing huge amounts of genomic data locally. The initial alpha rollout will be limited to a small set of users. Based on our experience supporting the GATK user community, we think this will dramatically lower the barriers to top-notch genomic analysis capabilities, especially for researchers who don’t have access to the kind of dedicated compute infrastructure and engineering teams required for analyzing genomic data at scale.

Rest assured, if you’re the do-it-yourselfer type, the DIY GATK option is still here; you’ll still be able to download the latest version of GATK from the Broad website, set it up on your own system and run it locally. We will continue documenting and supporting this option with the same level of dedication as ever.

You can read more about the details in the Broad Institute press release and on the Google Cloud Platform blog. Feel free to ask questions in the comments thread of course. We’ll keep you posted here as we move forward.


Workshop presentations -- 2015 Pretoria, South Africa 6/22-26 Jun 22

The slides from the workshop presentations as well as related materials will be posted here at the end of each day:

https://drive.google.com/folderview?id=0BwTg3aXzGxEDVk5RcEF3WW1SQWM&usp=sharing


Website down for server maintenance over the weekend Jun 13

The GATK website will be down at some point over the weekend between Saturday and Sunday night due to maintenance operations on the Broad servers. We don't know exactly what will be the time and the duration of the outage -- hopefully it will be brief.

The forum itself (including the documentation articles) will remain available, although the styling and layout may be affected.

Apologies for the late notice.

Have a great weekend and we'll see you on the other side.


Update to the accelerated PairHMM library for IBM POWER8 systems Jun 2

The Ubuntu version of the library provided by IBM to accelerate HaplotypeCaller on their POWER8 systems (originally described here) has been updated to fix a bug. You can download it from the original DropBox link.


Holiday notice -- forum on hiatus, service resumes May 26 May 23

As the USA will be observing Memorial Day on Monday 25, forum support will be (mostly) unavailable until Tuesday 26.

I say mostly because some of us have been known to sneak away from friends and family to secretly answer forum questions on their smartphone. Which is terrible social etiquette and must be strictly discouraged, of course.

To anyone in the USA and abroad who will be enjoying a long weekend, have a great time, and do spare a thought for the men and women whose service and sacrifices we honor on this occasion.

To the rest of y'all, sorry folks! But I'm sure you have holidays we don't have :)


Version highlights for GATK version 3.4 May 22

Folks, I’m all out of banter for this one, so let’s go straight to the facts. GATK 3.4 contains a shedload of improvements and bug fixes, including some new functionality that we hope you’ll find useful. The full list is available in the detailed release notes.

None of the recent changes involves any disruption to the Best Practice workflow (I hear some sighs of relief) but you’ll definitely want to check out the tweaks we made to the joint discovery tools (HaplotypeCaller, CombineGVCFs and GenotypeGVCFs), which are rapidly maturing as they log more flight time at Broad and in the wild.


Read more...

Release notes for GATK version 3.4 May 15

GATK 3.4 was released on May 15, 2015. Itemized changes are listed below. For more details, see the user-friendly version highlights to be published soon.

Note that the release is in progress at time of posting -- it may take a couple of hours before the new GATK jar file is updated on the downloads page.


Read more...

Workshop presentations -- 2015 UK 4/20-24 Apr 19

The presentation slides from the 2015 "GATK in the UK" workshop (April 20-24) are available on DropBox here.

All slides will ultimately be posted in the Presentations section of the Guide.


GATK licensing through Broad starts today Apr 16

It’s official! As of today, we are able to offer commercial licenses for GATK and MuTect directly through Broad. Stay tuned for details of terms & conditions, coming soon to this very blog.

In the meantime, please email softwarelicensing@broadinstitute.org with any questions or to purchase or renew a license.


The GATK support team is hiring! Apr 8

You've got basic experience with GATK, MuTect, Picard or related genome analysis tools, and a burning desire to help enable great science for a living? Join us now by applying for job #1774 on the Broad careers web page.

The job in a nutshell:

  • Work closely with method developers and software engineers to ensure user proficiency with analysis software, diagnose and/or resolve user issues, and provide scientific/technical support;
  • Create and maintain web-based technical documentation, tutorials and FAQs;
  • Organize workshops to train users in best practices and general workflows;
  • Perform analyses demonstrating the value of the tools for the user community.

But don't be fooled by the dry description -- this job offers variety, challenge and plenty of opportunity for growth. See my personal perspective/pitch below!


Read more...


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GATK Dev Team

@gatk_dev

@stevesmithcam @drchriscole Why would you ever not ;-D
26 Jun 15
@drchriscole @stevesmithcam Send 'em our way, we'll give them a primer to hit the key points. It's not rocket science ;)
26 Jun 15
RT @dgmacarthur: Should we bother switching from B37 to B38 as the human reference genome? http://t.co/FhkDHoSXck I'm in no hurry.
26 Jun 15
RT @BroadGenomics: A very Happy 3rd Birthday to Broad Genomics! Here's to many more to come! http://t.co/HsrlWcFxll
25 Jun 15
RT @konradjk: @gatk_dev @dgmacarthur Cloud to Butt Plus! https://t.co/wJUpXmMFhM
25 Jun 15