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Created 2015-04-16 18:17:31 | Updated | Tags: license

Comments (14)

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.

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

Comments (12)

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 2014-09-02 04:41:02 | Updated | Tags: phone-home license gatk3

Comments (2)

We've made a few minor updates to the license text as follows:

  • Updated the major version number from GATK2 to GATK3;
  • Updated the Broad address from 7 Cambridge Center to 415 Main Street (simple renaming, no move involved);
  • Added an explicit mention of the Phone Home reporting feature (which you can read more about here);
  • Clarified the terms relative to third-party contributions to protected code (section 2.1 - Grant).

None of these changes should have any effect on anyone's ability to use GATK.

Created 2013-01-17 16:16:44 | Updated 2014-09-02 04:43:08 | Tags: license gatk-lite lite

Comments (65)

Note: the license has been updated for GATK 3.x. See details here.

If you never got the point of GATK Lite and you hated the 2.0 license... Oh, do we have good news for you!

First, a little bit of context. When we released GATK 2.0, the GATK had emerged as the leading research software package in its domain. Public demand for tech support was rising rapidly; not only from the academic research community as it had in the past, but also from researchers using the software in a for-profit context. These latter users have specific needs (quality assurance, process certifications, etc.) that we are ill-equipped to address.

This drove us to seek a partnership with a company called Appistry which could release and license the GATK as a commercial software product appropriate for use in a for-profit and regulatory-compliant setting. We knew this solution would better meet customer needs, while alleviating our support burden and allowing us to focus on our core constituency, the academic and non-profit research community. This plan also had the prospective benefit of leveraging the intellectual property of the GATK (much of which results more or less directly from public investments) to fund the continuation of our research and development activities.

However we knew it would take us and our partners at Appistry some time to develop a mature commercial product. So as an interim solution, we enacted a more restrictive license, closed part of the source code on the “Full GATK” release, and provided a “Lite” version to enable for-profit users to keep working with an up-to-date version of the GATK (albeit without the cutting-edge tools that were introduced in version 2.0). Of course, the GATK programming framework (the GATK engine, libraries, and basic data management tools) continued to remain open source under the MIT license.

Well, we got a lot of feedback from the user community over these changes. We listened carefully, took the criticism to heart, and realized our interim solution left much to be desired. First, closing part of the source code was a deeply unpopular move. Many of you pointed out that this might restrict academic knowledge and obstruct progress in the field of algorithmic research. Second, we did a poor job of communicating the purpose of Lite and how it differed from the Full version. Even though Lite was always intended as an interim solution, some organizations opted to adopt it instead of the Full version and seem to view it as a viable long-term solution for genetic analysis. Related to this, we found that maintaining the two different distributions gave us our share of headaches in terms of supporting and updating the toolkit.

In light of these considerations, we’re going to change things up again, hopefully for the better!

In a nutshell: no more Lite and a new license (attached) that restores free access to the source code for those in the community performing academic non-commercial research. That’s right, free as in beer! You’ll still have the option of downloading the packaged binary (i.e., the “ready-to-run” program) from our website as you did before, but you’ll also be able to get the full source code (programming framework AND all tools including the latest and greatest) straight from the Github repository if you want. You can set it up on a server and provide it as a service to other non-profit users within your organization. You can dig into our deepest secrets to find out what makes ReduceReads and the HaplotypeCaller tick. And feel free to send us patches if you find a way to improve the code!

Licensed users through Appistry, in addition to having access to the full GATK and the added benefits of a fully-fledged commercial solution (less buggy, more help-y), may optionally purchase access to the source code. Appistry has been fine-tuning its process for providing the commercial product (including enterprise-grade QA, which we don’t do) as well as training a professional support team. If your use of GATK requires a commercial license, we encourage you to reach out to them. Appistry will be able to handle any questions you may have about the commercial release schedule, available support, and of course, licensing and pricing terms (whether for individual or site-wide licenses, companies big and small).

The following figure summarizes the different packages and their corresponding licenses.

Note that if you are using a version of GATK-Lite, you may continue using it, but we will be making no more updates to Lite after 2.3. Thus, if you choose to stay with Lite, you will be using an outdated version of the toolkit and you won’t benefit from any further improvements made to the GATK with the 2.4 release and in the future.

We welcome any and all comments on these new changes, which are due to take effect with the upcoming release of version 2.4 (tentatively scheduled for early February). There’s still time to tweak the language of the license if you spot any issues we’ve overlooked.

If you are using the GATK in an academic or non-profit research setting and have any questions or concerns about the details of the new license (attached), please join the discussion in the comments below. If you are using the GATK in a for-profit context, please contact our partners at Appistry as they will be in a better position to address your questions. If you’re not sure in which category you belong, please contact either Appistry or Issi Rozen at the Broad Institute.



  1. Removed "free as in speech" since the distribution of modified source is restricted to within academic institutions.

  2. Add a link in-text so people can see the license text without registering.

  3. Added a TXT format version for those who don't want to use DOC.

  4. Corrected the license file version.

  5. Prepended note and link to the license updates for GATK3 (9/02/14)

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

Comments (0)

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.

Created 2016-04-08 17:18:27 | Updated | Tags: license

Comments (3)

As suggested I requested licensing by emailing softwarelicensing@broadinstitute.org. I have done this twice since Monday (Apr 4 2016) and I have not received a reply yet. What do I need to do to renew my institution's license?

Created 2015-10-05 09:01:39 | Updated 2015-10-05 09:02:00 | Tags: license

Comments (1)


I submitted a licensing inquiry to softwarelicensing@broadinstitute.org on the 17th of September and a follow up on the 22nd. Does anyone monitor that address? I'd appreciate someone getting in contact with me to discuss our requirement for a license and the cost.


Created 2015-06-29 14:01:45 | Updated | Tags: license

Comments (1)

GATK team,

I hope that this question has not been asked too many times before, but I did not find it on the forum and apologize in advance if I missed it. I just wanted to get clarification from the Broad Institute on the license terms regarding GATK.

First am I permitted, as a system administrator, to agree to the GATK software license and install the software into a common area on our HPC cluster for intra-institution use.

Second, is the GATK resource bundle on the public FTP server under any licensing restrictions that I should be aware of?


Created 2014-03-19 14:45:03 | Updated | Tags: license

Comments (1)

The license still refers to GATK2 in several places. For example:

"1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE."

Not sure if this is intentional, but might want to update it for clarity, or better still eliminate all reference to version in the license.

Created 2013-11-14 19:55:16 | Updated | Tags: license gatk

Comments (6)

I have been asked to reach out to you to clarify the GATK license. We are hoping to package our CNV/SNP calling and annotation pipeline that includes GATK and make it available on an Amazon Machine Image (AMI) for use on the Amazon EC2 cloud for anyone who wants to replicate our protocol using their own data. Of all the tools that we use, only GATK contains license restrictions. It is our intent that our AMI be used by academic/non-commercial users, and it is not intended to be sold. We can list the AMI in the AWS Marketplace as a Bring Your Own License (BYOL) instance. However, there are no checks provided by Amazon that users do in fact have a license. Is this permissible?

Created 2013-10-30 08:31:12 | Updated | Tags: license workflow graphics permission

Comments (3)

I have used GATK in my PhD project, and was wondering if I could get the permission to use the Best Practices workflow graphics [1] in my doctoral dissertation? How should I attribute your copyright?

[1] http://www.broadinstitute.org/gatk/img/BP_workflow.png

Created 2013-03-12 14:01:12 | Updated | Tags: test license development resources

Comments (3)

I have two licence questions. First of:

There are two licence notes in BaseTest.java. I'm assuming that the top one is the one that should be viewed as currently in use. Is this correct?

Secondly, under which licence are the test resources made available. Am I'm free to use and redistribute these? I'm asking since I'm in the process of refactoring my pipeline project to use GATK as a external dependency, but some of the tests I've written use the files provided with the GATK as a resource, and I'd like to keep them and distribute them with the project as I've done before in my GATK fork.

Created 2012-09-06 07:39:56 | Updated 2012-09-06 14:26:04 | Tags: gatk2 license

Comments (4)

Dear Sir,

We are keen to know more regarding the licensing arrangements for GATK 2.0, specifically availability and cost. I understand not all arrangements are yet in place, however we are eager to receive any updated information you may have. Please may I request contact information so that we may continue this discussion via telephone.

Thank you for your assistance. Kind regards,

Ian Roberts.

PopulationGenetics Cambridge UK www.populationgenetics.com

Created 2012-08-02 20:19:28 | Updated 2013-01-07 20:13:18 | Tags: gatk2 license

Comments (42)

This discussion was created from comments split from: GATK 2.0 announcement. This was done because the new licensing and mixed open source model has turned out to be the object of much debate. We want to encourage discussion on this topic without obscuring the GATK 2.0 announcement thread, which is dedicated more so to the GATK 2.0 software itself, particularly the new tools and improvements. So, have at it!