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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.


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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.


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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!


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GATK and MuTect licensing moves to direct-through-Broad model Apr 2

We have some important news to share with you regarding the licensing of GATK and MuTect. The licensing agreement between us and Appistry will end effective April 15, 2015; from that point on, the tools will continue to be licensed through Broad for commercial entities that will be running the GATK and MuTect internally or as part of their own hardware offering. Current licensed users will transition to Broad Institute when their current license expires.

For our academic and non-profit GATK and MuTect users, the licensing transition will be essentially transparent. You will still be able to use the GATK and MuTect for free, and access the source code through the existing public repository. The support forum and documentation website will also remain operational and freely accessible to all as they been previously.

Since our commercial users will now get their license --and their support!-- directly from Broad, they can expect to see some clear benefits:

  1. Better access.
    We have heard from our licensed user community that you would like greater access to the GATK support team. Licensing through Broad will remove intermediaries and allow all GATK and MuTect users --including those who purchase a license-- more direct contact with and support from our team.

  2. Most current tools. Getting your GATK license through Broad license will give you access to the most cutting-edge tools and features available without sacrificing support. Under Broad licensing, you will still have the option of purchasing a license for either of two packages, “GATK” or “GATK + Cancer Tools”.

  3. Up-to-date Best Practices recommendations.
    You will get our latest recommendations, informed by the latest in our internal analysis and internal R&D work, directly from us. So you can be confident that you have access to the freshest information at all times.

Our development team is driven by the goal of building tools to enable better science and push the boundaries of genome analysis. Revenue from GATK and MuTect licensing enables these goals by directly feeding into GATK and MuTect development, in the form of critical codebase maintenance and bug fixing work, as well as expansion of the support team. This enables us to keep pace with the growth of the user community and the ever-increasing demand for GATK and MuTect support.

This is a significant new milestone in the life of GATK and MuTect, and we recognize that there are going to be a lot of questions and discussions on this topic since it will affect many of you in the research community. We’ve put together some FAQs (below the fold) that we hope will answer your most pressing questions; feel free to comment and suggest additional points that you think should be covered there.

Note that we are still working on defining some of the finer points of the support model and pricing structure, so we can’t address those quite yet -- but feel free to email softwarelicensing@broadinstitute.org if you have some burning question and/or concern that you’d like to discuss regarding licensing and/or pricing in particular. Rest assured that once the model has been finalized, we will make the full details (including pricing) available on our website in order to ensure full transparency.


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Workshop presentations -- 2015 BroadE 3/19 Mar 19

The slides from the 2015 BroadE GATK Best Practices workshop presentations are accessible at this Dropbox link.

The video recordings of the workshop talks are online here. We'll post links to the videos (along with copies of the corresponding slides) in the Presentations section of the Guide. They will also be available on the Broad's YouTube and iTunesU channels.


Consolidating GATK + Picard tools support Mar 9

Here's some good news for anyone who has been using both GATK and the Picard tools in their work -- which means all of you, since you all follow our Best Practices to a tee, right?

As you may know, both toolkits are developed here at the Broad Institute, and are deployed together in the Broad's analysis pipelines. The fact that they have been developed, released and supported separately so far is more an accident of history and internal organization than anything else (and we know it's inconvenient to y'all).

The good news is that we're taking steps to consolidate these efforts, which we believe will benefit everyone. In that spirit, we have been working closely with the Picard tools development team, and we're now ready to take the first step of consolidating support for the tools. From now on, you will be able to ask us questions about the Picard tools, and report bugs, in the GATK forum. And developers will be happy to hear that we are also committed to supporting HTSJDK for developers through the Github repo’s Issues tracker.

In the near future, we will also start hosting downloads and documentation for the Picard tools on the GATK website. And before you ask, yes, the Picard tools will continue to be completely open-source and available to all free of charge.

To recap, we have brought the GATK and Picard teams together, and we are working on bringing together in the same place all the methods and tools to perform genome analysis. Our goal is to make a world where you can run our complete Best Practices pipeline end-to-end with a single Broad toolkit. We think it’ll make your life easier, because it sure is making ours easier.


Registration open for GATK workshop (March 19-20) Feb 23

Registration is now LIVE for our upcoming BroadE Workshop: Best Practices for Variant Calling with the GATK.

WHEN: Thursday, March 19 & Friday, March 20, 2015

10:00 AM - 5:00 PM (Lecture, March 19)
2:00PM - 5:00 PM (Optional Tutorial, March 20)

WHERE: Broad Institute

Auditorium (lecture)/Yellowstone (Tutorial)
415 Main Street
Cambridge, Massachusetts 02142

Registration Schedule:

Registration closes February 27 at 5:00 PM.
Notification of acceptance or wait list status sent by March 4.

REGISTER HERE


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GATK Dev Team

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Holiday notice -- #GATK forum on hiatus for Memorial Day weekend, service resumes May 26. https://t.co/uVpA8SSXdl
23 May 15
Detailed version highlights for #GATK 3.4, better late than never... https://t.co/5BxNB0rVwv
22 May 15
RT @dgmacarthur: Users should not accept "black box" approaches from bioinformatics companies: http://t.co/uVQik8reDm
21 May 15
@MattBashton It's related to that, yes.
15 May 15
RT @fdmts: Senior position @broadinstitute with data sciences ops team. http://t.co/RF5ftrPu5O, job req 1635. #bigdata #genomics #hiring
15 May 15