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

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited April 2015 in Announcements

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 [email protected] 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 [email protected]. 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 [email protected]. 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.

Post edited by Geraldine_VdAuwera on


  • chapmanbchapmanb Boston, MAMember ✭✭

    Thanks for the updates on licensing and support. I'm excited that you're considering changing the restrictions around re-distribution of GATK. We work on a open-source framework that optionally uses GATK and MuTect for variant calling and it requires specific code and manual steps by users for both a local automated installation and Docker-based installations:


    It would be brilliant if we could re-distribute the GATK and MuTect jars in an automated way along with the rest of the tools to avoid this. Our goal is to make it easier to use GATK and MuTect, so anything we can do to make this easier for biologists using it would be helpful. Thanks again.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @chapmanb, I'm glad -- this had been emerging as an important use case that we had no plan for, so I'm really looking forward to us finally having a solution for this. Would you mind getting in touch with us directly by email to discuss options? I'm vdauwera at broad.

  • ekanterakisekanterakis UKMember

    What a great relief! I truly believe that the Broad can do much better in the commercial front and should take this responsibility on directly. There is understanding from the community that GATK and MuTect are complex software workflows so promising a "push-button" solution is not the way to go. The forums and yourself (Geraldine) above all have done a great job at providing relevant help where it's needed. In my experience, the previous commercial partner was not adding value on top of that and in many cases was further obfuscating the process. Thank you!!

  • coldrecdcoldrecd Member

    I'm encouraged by this as well. My email to the linked address failed:

    To: "[email protected]"
    [email protected]
    Subject: Please keep me updated on GATK license info
    Hello [email protected],

    We're writing to let you know that the group you tried to contact (softwarelicensing) may not exist, or you may not have permission to post messages to the group. A few more details on why you weren't able to post:

    • You might have spelled or formatted the group name incorrectly.
    • The owner of the group may have removed this group.
    • You may need to join the group before receiving permission to post.
    • This group may not be open to posting.

    If you have questions related to this or any other Google Group, visit the Help Center at http://support.google.com/a/broadinstitute.org/bin/topic.py?topic=25838.


    broadinstitute.org admins

    And thank you right back!

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I am not sure if I helped, but I just verified your account. Please try again and let us know if it still does not go through.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi all, the email bouncing is a small technical issue in how the email address was set up. We'll get this fixed asap. We'll let you know when it's fixed, as we look forward to your emails :)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    edited April 2015

    FYI all, the contact email, [email protected], has been fixed.

  • thondeboerthondeboer Redwood City, CA, USAMember ✭✭

    Glad to see the Broad came to its senses! We may still be interested in a commercial license...Will the license fee be any lower since Appistry was just way too expensive for us at ArcherDX...

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @thondeboer,

    I really can't comment on pricing at all just yet -- as long as the agreement with Appistry is in play (until 4/15 included), it's important that we respect their ability to conduct business without undue influence from us.

    What I think I can say, from being involved in the development of the new plan -- which is an exciting new twist for this tech support monkey! -- is that I'm really looking forward to the show & tell, because I rather expect that anyone who's feeling at least cautiously optimistic will not be disappointed. And now I'll shut up before I get myself in hot water with the lawyers :)

  • PepetideoPepetideo Member ✭✭

    Having been one of the vocal critics of the broad institute when then decided to offload licence fee paying customers to an external entity I'm glad that you have now corrected course.

    I still do not know how much the licencing is going to cost so I'll reserve judgement on that part. But it always struck me are a clear error on the broad institute to rely on an external company to support the very people that would be the financial backbone of the product especially when the licence fee was in my own opinion really excessive for small and medium enterprises.

    Great news... So far.

  • coldrecdcoldrecd Member

    Hi Geraldine and Sheila:

    I've contacted [email protected] again and while my mail did not bounce, I've yet to receive a reply.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @coldrecd, feel free to resend to me (vdauwera at broad) and I'll make sure you get an answer.

  • kmhernankmhernan Chicago, ILMember

    I tried to send an email to @Geraldine_VdAuwera but it bounced. I wanted to see what the state of using GATK in docker for an open sourced pipeline. Are there any updates?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @kmhernan, I should have clarified that the email domain is @broadinstitute.org (trying to avoid automated spambots...).

    Are you asking whether it's okay to include GATK in the docker image of a pipeline that you wish to distribute? In general that is not allowed under the academic license; however we can give permission to do so on a case by case basis if the docker image is meant to accompany a specific publication, in the interest of promoting reproducible research. However, the GATK jar itself can't be checked into an open source repository.

    For the general case, where you have an open source project that calls on GATK, the current rule is that you need to instruct users to get their own copy of GATK and plug it into the project as appropriate. We realize this can be burdensome, and so we are planning to publish GATK docker images in DockerHub that projects will be able to call on for this sort of purpose. This will happen in the very near future.

    Does either option sound like a solution to what you'd like to do?

  • kmhernankmhernan Chicago, ILMember

    Thanks @Geraldine_VdAuwera ... for now I can definitely have the GATK bits not in a docker and have the users install on their own (which is how we did it for v1 of the pipeline). I am definitely interested in the dockerhub when it's ready!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We'll post an announcement on the blog when the dockerhub is ready for primetime. It's a matter of weeks -- we're just waiting for some dev time to free up to actually get it done.

  • sherey65sherey65 SeattleMember

    Any news on the upcoming dockerhub announcement (or the expected timing thereof)?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @sherey65, we have someone assigned to this but he's been fighting some fires. If things calm down in the next week or so we can hope to have the dockers in hand sometime mid-November. But no guarantees.

  • sherey65sherey65 SeattleMember

    Just checking in again ... any updates on GATK availability on dockerhub?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @sherey65 Sooo things didn't calm down and it's not done :-\ But we've reassigned the task to someone marginally less busy. Sorry for the ongoing delays.

  • sherey65sherey65 SeattleMember

    checking in again -- any news now that it's February?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Is it already? Yikes.

    OK, so our current status is that we have GATK versions 3.5 and 3.6 (and an alpha version of GATK4) publicly available on Dockerhub in the docker image used by our production pipeline (https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/).

    We also have a plan to make every version of GATK available by itself through Dockerhub. We've been wanting to do this for awhile but haven't been able to prioritize it. Right now our focus is on an upcoming workshop, for which we're developing some brand new material (MuTect2 and WDL pipelining) so the "individual docker for every version of GATK" project will probably happen at some point in March. Hopefully March 2017 :)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Updating this for the record: we know have official dockers for individual versions; GATK4 versions are at https://hub.docker.com/r/broadinstitute/gatk and GATK 3.x versions are at https://hub.docker.com/r/broadinstitute/gatk3.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Also want to say for the record, for the benefit of anyone who missed the announcement earlier this year, GATK4 (currently in beta, due to be released into general availability Jan 9, 2018) is completely open-source under BSD 3-clause.

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