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Created 2015-04-02 07:14:02 | Updated 2015-04-02 21:14:59 | Tags: license appistry topstory

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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.

Frequently Asked Questions

Who is impacted by the licensing transition and how?

Academic/non-profit users: No change. The licensing terms remain the same and the GATK remains free to use for not-for-profit research and educational purposes. The current free user support model will remain available through the online forum.
Currently licensed Commercial/for-profit users: Appistry will continue to provide full GATK support for the remainder of your current license term. After that point, Broad Institute can offer you a GATK license directly. This will offer you immediate access to the latest version of GATK. We can work directly with you on your specific licensing questions at softwarelicensing@broadinstitute.org. For support questions, GATK product upgrade information or other suggestions, please comment in the discussion below or send us a private message.
Prospective commercial/for-profit users: Broad Institute can offer you a GATK license directly. This will offer you immediate access to the latest version of GATK. We can work directly with you on your specific licensing questions at softwarelicensing@broadinstitute.org. For support questions, GATK product upgrade information or other suggestions, please comment in the discussion below or send us a private message.

Will licensed users (commercial / for-profit) and non-licensed users (non-profit and academic) have access to different versions of GATK?

No. There will only be one version for all users. We will provide our licensed users total support for the very latest version. This means they will always be able to use the most cutting-edge tools and features available without sacrificing support.

Now that the Broad's licensing agreement with Appistry is ending, why not make GATK free for commercial users, just like it is for academic/non-profit users?

Part of the Broad Institute’s mission is to share our tools and research as broadly as possible to enable others to do transformational research. We started developing GATK several years ago and, since then, have constantly upgraded it, thanks to the hard work and dedication of many talented programmers, developers and genomic researchers in our group and beyond. That is why GATK remains the most advanced, accurate and reliable toolkit for variant discovery available anywhere (if we do say so ourselves). But please understand that building, maintaining, testing and constantly improving GATK is neither easy nor free. This is why we charge commercial users a licensing fee and funnel these resources back into upgrades of the tool itself – it allows us to continue to offer GATK for free to academic and non-profit organizations while ensuring it is always the best-of-the-best in an emerging and rapidly-changing field of research.

Will Broad offer only GATK as a licensed product or will there be an equivalent to the Cancer Genomics Analysis Suite offered by Appistry?

In addition to the GATK package, we will also offer a package that bundles GATK with MuTect and ContEst. That package will not include the SomaticIndelDetector, but a replacement for that functionality is in preparation.

A recent announcement indicated that Picard tools will be integrated into future versions of GATK. Does that mean tools that originated in Picard will be subject to the protected GATK license?

No. Tools originating from the Picard toolkit will remain free and fully open-source for everyone. We are preparing to integrate them into a part of GATK that will be under a BSD license.

Will researchers who develop and publish analysis pipelines involving GATK be allowed to bundle GATK in, e.g., any Docker images that they provide to the community?

We are preparing to enable this in order to facilitate sharing of scientific methods, but we need input from the community first. To that end, we’d like to invite researchers who are developing or have developed such pipeline images to contact us in order to discuss options. We are envisioning simple technical solutions to ensure that users of these images are made fully aware of their own legal responsibility relative to the GATK licensing status, in a way that minimizes the burden on the researchers who distribute them.

Created 2014-11-05 18:45:56 | Updated | Tags: appistry webinar versions

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Our partners at Appistry are doing another free live webinar tomorrow (Nov 7), this time focusing on the differences between versions of GATK. The ultimate point is, of course, to convince any stragglers to upgrade to the latest and greatest major version series (GATK 3.x for those of you following at home) but unlike us, they will actually take the time to explain in detail why this is a winning proposition.

If you have any questions about the differences between versions, be sure to register today and tune in tomorrow, Thursday 7 November at 12 pm EDT. Anyone can join (not just Appistry customers) so don't miss this great learning opportunity. Every question will be answered, either during the live event or by email afterward if they run out of time.

Created 2014-08-15 09:41:46 | Updated | Tags: appistry rnaseq webinar

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Our partners at Appistry will be doing a webinar on RNAseq analysis next Thursday. The webinar will include a live presentation of the complete pipeline for RNAseq analysis, as well as question time open to all participants. As usual it's free and open to all, you just need to register at Appistry's website. Check it out!

Created 2014-07-23 17:04:25 | Updated | Tags: appistry challenge competition

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Creative minds, your attention please -- our licensing partners, Appistry, are holding a competition! From the Appistry Pipeline Challenge webpage:

The Appistry Pipeline Challenge will reward and support one winning proposal for a creative pipeline that will make a difference in clinical research and precision medicine. We’ll provide the winner with a complete NGS analysis package valued at $70,000 including commercial-grade bioinformatics tools for variant calling and somatic mutation analysis, software and hardware for developing and executing pipelines at scale, and a year’s worth of support so that you can make your idea a reality.

There's more detailed information on the contest webpage of course, and if that doesn't answer all your questions, Appistry is holding a live webinar tomorrow (Thursday 7/24) to give additional details and answer questions.

The deadline for submissions is August 15th, so if you have an idea, better get on it!

Created 2014-04-10 17:39:08 | Updated | Tags: video presentations appistry webinar slides gatk3

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The slides from today's webinar are available as of now in the GSA team Dropbox at this link, and will be on the documentation website shortly.

Created 2014-04-04 01:48:46 | Updated | Tags: appistry rnaseq webinar gvcf gatk3

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Our partners at Appistry are putting on another webinar next week, and this one's going to be pretty special in our view -- because we're going to be doing pretty much all the talking!

Titled "Speed, Cohorts, and RNAseq: An Insider Look into GATK 3" (see that link for the full program), this webinar will be all about the GATK 3 features, of course. And lest you think this is just another marketing pitch (no offense, marketing people), rest assured that we will be diving into the gory technical details of what happens under the hood. This is a great opportunity to get the inside scoop on how the new features (RNAseq, GVCF pipeline etc) work -- all the stuff that's fit to print, but that we haven't had time to write down in the docs yet. So don't miss it if that's the sort of thing that floats your boat! Or if you miss it, be sure to check out the recording afterward.

As usual the webinar is completely free and open to everyone (not just Appistry customers or prospective for-profit users). All you need to do is register now and tune in on Thursday 4/10.

Talk to you then!

Created 2013-12-02 22:37:28 | Updated 2013-12-02 22:38:04 | Tags: appistry webinar

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Our commercial partner, Appistry, is announcing a webinar about the tools from the Broad Institute that Appistry distributes. They will review improvements to the GATK in 2013, provide an update on all of the components of Appistry's Cancer Genome Analysis Suite, and introduce ContEst, the newest extension to the CGA Suite. You'll also get a preview of Appistry's plans for delivering new Broad NGS analysis tools in 2014.

You can register for this free webinar, which is open to all (not just current license holders) on Appistry's website.

Created 2013-10-28 18:14:01 | Updated | Tags: appistry commercial webinar

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Our commercial partner, Appistry, is announcing a webinar on the commercialization of GATK. They will discuss the Broad-Appistry relationship, the current status of the commercial GATK product (including licensing options), and plans for the future (including expansion to other Broad tools, with a focus on cancer research).

You can register for this free webinar, which is open to all (not just current license holders) on Appistry's website.

Created 2013-10-01 00:55:10 | Updated 2013-10-01 14:24:41 | Tags: mutect appistry webinar cancer

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Our partner Appistry (who distribute GATK and MuTect to commercial users) will be holding a webinar on 3 October. Registration is open to all; you can find more details on the Appistry website here:


Created 2013-07-24 20:26:27 | Updated 2013-07-26 14:41:56 | Tags: mutect appistry gatk webinar

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Heads up, cancer researchers! Appistry (our commercial licensing partner for GATK and now MuTect) is announcing an upcoming webinar on best practices for somatic mutation studies using GATK and MuTect. Registration for the webinar is open to all (not just Appistry customers) so be sure to sign up for this. See the announcement on Appistry's website for more detailed information.

Created 2013-04-08 17:33:44 | Updated 2013-04-08 17:34:22 | Tags: appistry

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Our commercial partner, Appistry, is holding a web-based seminar on how to apply GATK Best Practices. This webinar is open to all (even if you're not a customer) so it's a great opportunity to learn about the Best Practices and the latest improvements to the GATK tools.

From Appistry's announcement:

The webinar will include details about how the best practices workflow is enhanced by the advanced functionality for NGS introduced last fall with GATK 2.0 and expanded upon in the latest release of the GATK from Appistry.

Attend this webinar to

  • Discover the optimal workflow for variant calling
  • Determine which GATK tools to use when
  • Learn the differences between the GATK’s two variant calling tools
  • Hear about the latest additions to the GATK

You can find out more and register for this webinar on Appistry's Events page.

Created 2012-10-16 13:56:33 | Updated 2012-10-16 14:05:37 | Tags: license appistry commercial

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As announced a few months ago, commercial users of the GATK will now be required to purchase a license in order to use the full-version GATK 2 for commercial / for-profit use (while GATK-Lite can still be used for any purpose without a license).

We are now able to give you more details about how this will work: we have selected a company called Appistry to be the exclusive partner who will handle for-profit GATK licensing and support. If you have any questions, please visit their FAQs page, and contact them directly to inquire about pricing or any "special case" scenario you feel may apply to your use of the GATK.

Appistry will launch a discussion forum within the next few days in which you will be able to network with your peers and Appistry staff about the for-profit release of the GATK.

If you would like to discuss why we have made these changes to the licensing model, please see our own discussion thread on licensing and source code models in GATK 2.

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