## Upcoming changes to the license & the retirement of GATK Lite by v 2.4

### Posted by Geraldine_VdAuwera on 17 Jan 2013 (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!

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.

--

Edits:

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

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

4. Corrected the license file version.

#### Pepetideo

It is great that you are returning to a full open-source model. This was always a contentious issue and I am glad you realised your actions were wrong and reversed course. However I would have to disagree when you say that companies, big and small can purchase a license for the software through APPISTRY. I am sure I cannot reveal prices here on this forum, but this is stretching to truth quite a bit since I have learned about the pricing structure of the license and it is NOT compatible with what I would define as a Small and even Medium sized company.

#### chapmanb

Geraldine; That's great news about open-sourcing the code for HaplotypeCaller and ReduceReads. Thank you for listening to the community response to GATK 2. Could you clarify which parts of GATK require obtaining a license for commercial use? Does this apply to all parts of the toolkit: variant calling, recalibration/realignment, and data management? Or can some functionality be used in commercial settings without a license? This distinction was clear to me with the GATK/GATK-lite toolkits. Now it sounds like the line is drawn somewhere between SelectVariants and HaplotypeCaller but I'm not sure where. My concern is that we develop open source pipelines that could be used in both academic and commercial settings. I'd like to be able to use GATK and give a clear distinction about which parts will require a license. Currently we do this via checking for full/lite: https://github.com/chapmanb/bcbb/blob/master/nextgen/bcbio/broad/__init__.py#L88 Will there be a way to distinguish in GATK 2.4? Thanks as always for the work on GATK.

#### pjacock

Sigh. The Broad appear to be stepping backwards here. As discussed on Twitter, the described academic non-commercial licence is NOT "free as in beer AND free as in speech" (as the announcement currently states). This is not "free as in speech". This is not Open Source. This would not be OSI approved. Free for academic use only licences are just trouble - for another thing at what point do you draw the line with things like joint projects funded by both government research councils and industrial partners being increasingly common? Originally GATK was open source (MIT), and all was well. Then you introduced a closed GATK v2 but continued the open source GATK v1 as "GATK Lite". People complained publicly, many saying they would reject the new terms and continue with other open source tools - this included researchers at the Sanger Institute. Now you're completely abandoning any open sourced version of GATK?! Also asked on Twitter: Why not follow the proven approach demonstrated by companies like RedHat - keep GATK under an open source licence, and sell commercial support as an option? http://storify.com/pjacock/gatk-v2-0-not-open-source

#### Geraldine_VdAuwera

> @Pepetideo said: > However I would have to disagree when you say that companies, big and small can purchase a license for the software through APPISTRY. I am sure I cannot reveal prices here on this forum, but this is stretching to truth quite a bit since I have learned about the pricing structure of the license and it is NOT compatible with what I would define as a Small and even Medium sized company. Hi Pepetideo, To be honest, we developers have no idea what the pricing structure is; that is all Appistry's responsibility. If it is so problematic, I recommend you talk to [Appistry](http://www.appistry.com/gatk/contact) about your concerns. I expect if they get enough people telling them this they may look for a solution that meets your needs better.

#### eparejatobes

Re @Geraldine_VdAuwera 1. companies (particularly so small ones doing a lot of R&D/pure research) are _made of_ individuals, which pay taxes too, as every other person :) 2. You can _choose_ whether you want to pay for company X's products and services. You're _forced_ to pay for BROAD developing GATK, in the form of taxes. 3. Not saying that this particular need (for Q&A, commercial support etc) doesn't exist; but this is _completely unrelated_ to licensing. In fact, if there's such a need, your move is actually a _negative_ one in that respect; In an open-source scenario, **any** company (not just Appistry) could provide support and a controlled release cycle, tests, whatever; and if there's really a market for that, they would do well. Instead, right now, what we have is a _monopoly_ in terms of offering such a thing to interested companies. 4. And, again, what about companies which do pure research? they're perfectly happy with the more "bleeding-edge" release style, but now they cannot use that, just because of _where_ they work? What's the difference between doing pure research for a salary (universities/public institutions), and doing pure research as a service (companies providing research-based services)? best

#### Geraldine_VdAuwera

> @eparejatobes said: > Re Geraldine_VdAuwera > 1. companies (particularly so small ones doing a lot of R&D/pure research) are _made of_ individuals, which pay taxes too, as every other person :) Um, we're not asking the individual employees to pay for the software, we're asking the company to pay for it. I'm sure we can agree there is a big difference there... > 2. You can _choose_ whether you want to pay for company X's products and services. You're _forced_ to pay for BROAD developing GATK, in the form of taxes. You're also forced to pay for cancer research, and you may never develop cancer yourself. You're also forced to pay for public transportation subsidies, which you may never use. You're also forced to pay for aid to foreign countries. You're also forced to pay for disaster relief in another state. That's part of living in a society where everyone pitches into the common pot, you don't always choose what the money goes to, but if it's run sanely, it evens out. > 3. Not saying that this particular need (for Q&A, commercial support etc) doesn't exist; but this is _completely unrelated_ to licensing. In fact, if there's such a need, your move is actually a _negative_ one in that respect; In an open-source scenario, **any** company (not just Appistry) could provide support and a controlled release cycle, tests, whatever; and if there's really a market for that, they would do well. Instead, right now, what we have is a _monopoly_ in terms of offering such a thing to interested companies. Keep in mind that there are other software packages that do the same thing, no one is forced to use the GATK. > 4. And, again, what about companies which do pure research? they're perfectly happy with the more "bleeding-edge" release style, but now they cannot use that, just because of _where_ they work? What's the difference between doing pure research for a salary (universities/public institutions), and doing pure research as a service (companies providing research-based services)? It's actually not at all about where you work, it's what the software is used for. If you are doing work that does *not* contribute to generating revenue, you can use it without a license. But companies providing research-based services make a profit off those services. At least I hope for them they do, or they need to revise their business plan! ;-)

#### Pepetideo

Well, in short, the broad institute has given their hard earned efforts in developing gatk to a single company that, for what I can gather, have complete control over over much they are willing to charge companies for using YOUR software! I do hope they have been payed handsomely for this privilege. Sad turn of events. I am predicting my company will be transitioning away from using GATK and like them most small and medium companies. We simply have no way of accepting what appistry is charging for a single user license. What happened to the idea of offering a GATK license to companies that would apply to have a "powered by GATK" style certification? That would probably bring in a lot of money and would require very little effort on your part

#### Pepetideo

> @Geraldine_VdAuwera said: > And if/when we do it, it won't be a "minimal effort" undertaking I did not mean it this a derrogative way. Apologies if it sounded that way. I was just referring that it would be rather straightforward to create a mechanism to certify some analysis pipelines to be compliant with you best practices in regards to GATK software.

#### Johan_Dahlberg

I have a question of practical nature in regards to paragraph 2.2 of the new licence. The licence states: > LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. I'm wondering how this relates to my (and the 40-or-so other) fork of GATK on github. Will the source released on github be restricted to the framework, or will it also contain the analysis tools? Does this mean that I will need written permission from Broad to host a publicly available fork or am I missing something here?

#### Geraldine_VdAuwera

> @Johan_Dahlberg said: > I have a question of practical nature in regards to paragraph 2.2 of the new licence. The licence states: > > I'm wondering how this relates to my (and the 40-or-so other) fork of GATK on github. Will the source released on github be restricted to the framework, or will it also contain the analysis tools? Does this mean that I will need written permission from Broad to host a publicly available fork or am I missing something here? Hi Johan, Re: access, the entire source will remain in github, so as long as you're using it for non-profit academic research you don't need to change anything. Not sure about the steps for having forks be public on github -- I will look into it and let you know.

#### priesgo

That was bad news for me. I'm in between the commercial and academic world and this change in policy kind of blocks our academic research as it goes accompanied and financed by commercial interests. About keeping to the last free (as in beer) version GATKLite 2.3, will you keep support in your forums? And if so, for how long?

#### Johan_Dahlberg

> @Geraldine_VdAuwera said: > Not sure about the steps for having forks be public on github -- I will look into it and let you know. As far as I'm aware there is no way to disable forking for a public github repository, so if free creation of public forks is not an option, I'm not sure that keeping the code on github will be an option. Personally, I think that it would be a step backwards to remove the option of accessing the code that way as it would make it more difficult for those of us who are (in a very modest way) contributing to the code base.

#### Geraldine_VdAuwera

> @Johan_Dahlberg said: > As far as I'm aware there is no way to disable forking for a public github repository, so if free creation of public forks is not an option, I'm not sure that keeping the code on github will be an option. Personally, I think that it would be a step backwards to remove the option of accessing the code that way as it would make it more difficult for those of us who are (in a very modest way) contributing to the code base. I agree. Rest assured that we appreciate your contributions to the framework and we remain fully committed to keeping the source on Github.

#### biomickwatson

Just read the post above mine to see my "use case" may well still fall under academic work. i) I would be very worried I would adopt this and then you change the license and I am screwed, and ii) I am still morally outraged that you're doing it at all

#### dswan

I think Mick's comment is especially true, the Broad seem to be changing their mind on things with every release, staggering from one idea to the next. Who is to say that in 6 months this isn't going to change again? Especially if Appistry fail to deliver on licence sales..

#### Mark_DePristo

While I certainly appreciate your concerns about open source, ownership of the project, and stability of our decisions, I don't think either of you will be satisfied with anything less than free (not just open) source software. We are of course happy if you'd like to use another software package, because of moral open/free software requirements or for the need for long-term project stability. Certainly if you want a purely open sourced data processing tool, you won't find it in the GATK. You are more than welcome to go out and create your own, or to use another already existing package; nothing is stopping you. Our view is that we need a commercial version of our software in order to support the many current and upcoming users who need long-term, commercial-grade software. We are under no obligations from our funders, or from anyone at the Broad, to commercialize the GATK. We are simply responding to a need for a more stable, better supported version of the GATK, and our view is that partnering with Appistry is the best way to accomplish this goal.

#### Geraldine_VdAuwera

@biomickwatson and @dswan : I sympathize with your anxiety about future changes. But please understand that this has been a transitional period for us too, and we've had to scale up from being a small team producing software internally for a fairly modest number of researchers within our institute, to serving thousands of researchers worldwide (but still as a [small team](http://www.broadinstitute.org/gatk/about/who-we-are)!). We made some mistakes in setting the original course six months ago, and now we're trying to make this work better. Would you really prefer us to stick with a flawed model even though we know we can serve people better by adjusting it, just in the name of not changing anything? We honestly don't want to have to make any more changes to our model after this, which is why this time we're asking for feedback before going through with it. If there's any aspect we can tweak to make it work better for people, we'll seriously consider it, even if we can't accommodate every request (a complete change of model is simply not going to happen).

#### biomickwatson

@Mark_DePristo Thanks for the response. I still don't really see why, if support is the issue, why you cannot adopt the model of charging for support (a la MySQL, Red Hat etc). I think time will tell if this is a smart move, however, my opinion (after 15 years in bioinformatics, in industry and academia) is that it is not. @Geraldine_VdAuwera I suspect samtools, bwa etc also support 1000s of users worldwide, and operate as free, open-source tools, supported by a small team. I just *do not* like this move. Bioinformatics, since it began, has been driven by free, open-source software. I will not support any move to change that, to be honest.

#### Geraldine_VdAuwera

> @chapmanb said: > it would make the transition less painful for those of us with a more open-source direction to consider increasing the proportion of the toolkit that is MIT licensed. This is not antithetical to your stated goals since the GATK-specific tools would still be dual licensed. Brad, you make a very good point here. I'm happy to report that after discussing this internally, we've decided to include the utility-type walkers in the MIT-licensed framework. Which means all walkers except the following core GATK-specific tools, which will remain dual-licensed (Broad/Appistry): - BaseRecalibrator - RealignerTargetCreator - IndelRealinger - ReduceReads - UnifiedGenotyper - HaplotypeCaller - VariantRecalibrator - ApplyRecalibration - VariantAnnotator annotation modules (not the walker itself) Will this help solve your problem?

#### Geraldine_VdAuwera

> @sarmadym said: > I'm not sure if Appistry actually does any additional QA. I had a few phone conference calls with them and asked them specifically what is your QA process and they seemed clueless about this and just responded with general terms like "we make sure that the package works". Well, I've met the person in charge of QA and I can tell you she knows her stuff. And she reads every post on this forum, so I expect she's going to go over and do a bit of QA on the sales people... EDITED: QA of course, not Q&A (I see Q&A everywhere, sorry)

#### pjacock

I'm finding this thread hard to follow because the original post keeps being update _without_ any notes to say what has changed. Just now I noticed even the figure has been edited - I'm sure the framework licence used to say "free - restricted", but now it says "MIT (free - open)". That is actually a very good change, as it appears the Broad is now continuing to provide the GATK core framework as open source software under the MIT licence. If that is true, then I am glad you're listening to the strong negative backlash against the original text where it appeared none of GATK would continue under the MIT licence.

#### Geraldine_VdAuwera

> @pjacock said: > I'm finding this thread hard to follow because the original post keeps being update _without_ any notes to say what has changed. Just now I noticed even the figure has been edited - I'm sure the framework licence used to say "free - restricted", but now it says "MIT (free - open)". I'm sorry but that is incorrect. The original post was updated only once and all the edits done at that point are listed at the bottom of the text. You can further see the details of the changes in the [change log](http://gatkforums.broadinstitute.org/log/record/discussion/2091). You'll see this lists three change "events" made immediately consecutive to each other. As for the figure, it has not been changed at all; the label for the framework has always read "MIT (free - open)". I can show you the original working documents if you'd like. > That is actually a very good change, as it appears the Broad is now continuing to provide the GATK core framework as open source software under the MIT licence. If that is true, then I am glad you're listening to the strong negative backlash against the original text where it appeared none of GATK would continue under the MIT licence. That is indeed the case, the core framework will continue to be under MIT license, *as stated in the original text (and figure) of this announcement*. The latest development, which is not as such reflected in the original text, is that we have decided to transfer "utility" walkers from the "protected" category into the framework in order to make them freely available. This we did in response to requests such as Brad Chapman's (above); and that is indeed the point of this entire exercise -- to collect feedback and amend our plan to suit a majority of users, before it goes into action.

#### pjacock

> @Geraldine_VdAuwera said: > I'm sorry but that is incorrect. The original post was updated only once and all the edits done at that point are listed at the bottom of the text. ... As for the figure, it has not been changed at all; the label for the framework has always read "MIT (free - open)". I can show you the original working documents if you'd like My apologies - I accept I was in error. I regret staying up late and commenting while tired. > @Geraldine_VdAuwera said: > You can further see the details of the changes in the change log. You'll see this lists three change "events" made immediately consecutive to each other. Actually I can't - the link http://gatkforums.broadinstitute.org/log/record/discussion/2091 says "Permission Problem - You don't have permission to do that.". Was there any link to the change log one the page prior to your comment? I think having an automated change logs or revision history for blog posts (once first published) would be a really good idea - something I think most readers would find familiar from their use in wikis.

#### chapmanb

Geraldine; That is brilliant. Thank you for listening, discussing with the group, and for the changes. It's incredibly helpful for me, and I hope will also help with continued open source use and adoption of the framework. The metrics and open-source geek part of me can't help but ask: why did you decide to include the annotations as part of the dual licensed? The annotator always struck me as one of the most useful place for community development, and I've made good use of annotators other folks wrote. Deriving from existing annotators you wrote is by far the easiest way to get started (PerReadAlleleLikelihoodMap and all, you know) which might become more complicated under dual licensing (I am not a lawyer). The decision on all the walkers makes good sense to me. Thank you again for listening. It's much appreciated.

#### Geraldine_VdAuwera

> @pjacock said: > Actually I can't - the link http://gatkforums.broadinstitute.org/log/record/discussion/2091 says "Permission Problem - You don't have permission to do that.". Was there any link to the change log one the page prior to your comment? > I think having an automated change logs or revision history for blog posts (once first published) would be a really good idea - something I think most readers would find familiar from their use in wikis. Oh, I guess you have to have admin privileges to see the log. I took for granted that everyone could see it, sorry. I'll see if it's possible to make the logs publicly accessible.

#### Geraldine_VdAuwera

> @chapmanb said: > That is brilliant. Thank you for listening, discussing with the group, and for the changes. It's incredibly helpful for me, and I hope will also help with continued open source use and adoption of the framework. Thanks, that is our hope as well. > The metrics and open-source geek part of me can't help but ask: why did you decide to include the annotations as part of the dual licensed? The annotator always struck me as one of the most useful place for community development, and I've made good use of annotators other folks wrote. Deriving from existing annotators you wrote is by far the easiest way to get started (PerReadAlleleLikelihoodMap and all, you know) which might become more complicated under dual licensing (I am not a lawyer). The decision on all the walkers makes good sense to me. The reasoning is that some of the annotators are key to certain core tools, so it makes sense for us to keep them under the same level of protection. But you make a good point about it being easier to derive new annotators from existing ones. I will see if we can release some of the annotators as examples for development at least. I do have a correction to make; in the list earlier I unintentionally omitted three walkers that will stay "protected" too: PhaseByTransmission, ReadBackedPhasing and DiagnoseTargets. My apologies; I hope this won't cause you any problems.

#### chapmanb

Geraldine; The annotations are also useful in other contexts for evaluating variants. I used them for [developing methods for filtering variant calls from multiple callers][1] and I'm sure there are other cool reuse ideas that are parallel to your key pipelines. I think this remixing is a critical component of improving bioinformatics tools. With the downstream tools protected, you can commercialize the pipelines you developed, while allowing others to experiment around the edges. I appreciate your willingness to discuss. I use GATK both with the best practice pipelines and to develop new tools, and it's great that you're open to allowing the continued experimentation and reuse of the framework. Thanks again. [1]: https://github.com/chapmanb/bcbio.variation

#### biomickwatson

There isn't enough room here, so I have put my thoughts on my blog: http://biomickwatson.wordpress.com/2013/01/28/gatk-why-it-matters/ I hope some of what I have written makes you think a little :)

#### TechnicalVault

On the whole being able to read the source code is better than not and the more objectionable portions of the license are gone so this makes it easier for me. It's not ideal but at least we can see what processes are being performed on our data. The one area I am slightly worried about however, is the situation with the Appistry and the source code. Can you confirm the Appistry GATK will be built from the same source code as the Broad GATK? This is obviously important because if I quote GATK version xxx.yyy.zzz against my academic copy, and someone reads that in a paper and tries to reproduce it on their commercial GATK it would be somewhat worrying if because of some slight bugfix made by Appistry the results delivered by their copy were different. Incidentally whilst I'm not sure I see why it would be in Appistry's interests to restrict their users from seeing the code behind their version if that code is the same as the Broad version (and I realise this is may not your decision). I could understand them wanting to charge for certifying any of their users customisations to the code so that they can be supported though.

#### pjacock

> @biomickwatson said: > There isn't enough room here, so I have put my thoughts on my blog: > > http://biomickwatson.wordpress.com/2013/01/28/gatk-why-it-matters/ > > I hope some of what I have written makes you think a little :) Likewise, http://blastedbio.blogspot.com/2013/01/free-for-non-commercial-academic-use.html

#### sjackman

I'd like to create a Homebrew formula for GATK, but the click-through license makes it impossible, since there doesn't seem to be a direct URL from which the source can be downloaded. Is there a direct URL?

#### Geraldine_VdAuwera

We have no plans to provide a direct URL, but when we release version 2.4 (this week or next) it will be possible to clone the full source code repository, which you can update directly via Git. If you're comfortable compiling from source that will be the most convenient way to keep your local install up to date.

#### TechnicalVault

> @Geraldine_VdAuwera said: > To address your concern, Appistry will provide the necessary documentation and support to licensed users to resolve any differences that occur between the academic and the commercial versions. If you could see fit to persuade them to commit to providing this information publicly that would be helpful; gain goodwill; lessen support burdens and cost them nothing. The scenario I envisage is a non-technical commercial user who is unaffiliated to myself trying to reproduce the results of my analysis which I produced using the academic version and published in a paper. There is an inexplicable difference in the results and they write to me to complain my results aren't reproducible. Because I am not a licensee I would not have access to the documentation so I wouldn't be aware of any differences that may or may not exist, nor can I reproduce their environment.

#### Geraldine_VdAuwera

> @TechnicalVault said: > The scenario I envisage is a non-technical commercial user who is unaffiliated to myself trying to reproduce the results of my analysis which I produced using the academic version and published in a paper. There is an inexplicable difference in the results and they write to me to complain my results aren't reproducible. Because I am not a licensee I would not have access to the documentation so I wouldn't be aware of any differences that may or may not exist, nor can I reproduce their environment. OK, I'll let Appistry know that this is a concern. But based on my interactions with many users including commercial ones I would expect that the commercial user would first go to Appistry's support and ask them why they can't replicate your results (and ask about version differences) before coming to you. When people aren't getting the expected results, they tend to first assume that the software isn't working properly, rather than question the expectations. I'm not sure what this means for science as such but from the point of view of your use case it should help fend off complaints...

#### sicotte

I am very happy. I have developed an external package PooledWalker (for analysis of Pooled DNA projects) to an older version of GATK (which requires compiling the whole GATK), so closing the source meant I could no longer publish it. I'll move it to the 2.3+ framework and publish it now.

#### Geraldine_VdAuwera

Glad to hear it! FYI you might want to wait another week until we release 2.4 to start fwd-porting, because we've moved some things around in the framework.

#### thondeboer

Thanks for the comments...I do know that the Broad is the one responsible for fixing the bugs etc. and it is good to hear that with the next release we will be up to par with the academic version, but I fear that once some bugs are detected in 2.4 (And let's face it, it sounds like quite a re-write of the framework, so there are bound to be some, pretty devastating ones in there), we commercial users have to wait a complete quarterly release cycle to get the bug fixes... In any case, since we are still on version 2.3-9, where is the LITE version? i can't see it on the main download page and it states that from version 2.4 LITE will not be available, but we ain't there yet! I have some tools i use sometimes from the LITE version that were broken in my commercial version (SelectVariants manges up the AD fields in some occasions) I would like to see if that is addressed in the latest version... Thanks, Thon

#### Geraldine_VdAuwera

Thon, you wound me... *devastating* bugs, really? I'll admit most of our releases come with a flurry of annoying little bugs and mishandled edge cases, but I don't believe we've *ever* let something you could qualify as *devastating* slip into a public release. The hyperbole is a little unnecessary, surely. In any case you'll be happy to know that the modifications we're currently making to the framework and toolkit ahead of 2.4 is not so much re-writing things as deploying an epic number of systematic tests, so release 2.4 should be our least buggy ever, to date. Personally I'm working on making significant changes to improve the Tech Docs *as a direct result of Appistry's QA process*, as well. Re: LITE version, that is in fact completely unintentional -- the updated "post-2.4" website changes were released early by mistake, so thanks for bringing that to my attention. It would be difficult to revert that now but I'll put up a link to the latest version archive. In the meantime you can follow [this link](https://github.com/broadgsa/gatk/archive/master.zip) to download the source archive and compile locally (ant dist). That is still all Lite, ie free to use for all, until we release 2.4.

#### thondeboer

Geraldine, I am sorry if I wounded you with my comment about devastating bugs...I did not intend that! I was merely speculating that it was a possibility as I suspected that a new framework was going to be a re-write...It is great to hear that 2.4 is more about implementing a large number of tests which will surely reduce the number of bugs I'm sure! I feel very hopeful for the new version...It's just that we commercial users have not been able to try any of the new functionality since 2.2-16 was the version we got and HaplotypeCaller was just not producing correct results, so we never got to determine if taking out a commercial license was of value to us... Trevor, I've send you an email to setup a conference call to discuss directly, but since Geraldine asked for public comments, I will continue to make my comments public :)

#### Geraldine_VdAuwera

Oh Thon, again with the drama? You're not banned from using the forum; it just so happens that I know you're a commercial user and are (or were) an Appistry customer because you've been a little bit... vocal about it. I have no insight into how long evaluation terms last, so I assumed yours was still running. But hey, if you're all done with Appistry and set on going forward with Lite, you're welcome to ask me questions again. I've got nothing against you, I was just enjoying being able to punt some of my workload to Craig :)

#### thondeboer

Yeah, we dutch guys are known for our drama :)...But all kidding aside, I just wanted to see clarified what the procedure is, since it is important for us to know where we stand with GATK...It's a significant part of my work at the moment but I am getting a lot of pressure from management to show it is worth all the drama :) So far it is!

#### Geraldine_VdAuwera

Hah, geen probleem, makker -- I'm Belgian. We're pretty chill. I'm happy to clarify any lingering questions -- or refer you to the appropriate person when I don't know the answer.

#### JTeer

Hi, Would you please point out the location for the last available "Lite" version? It seems with the 2.4 release, the lite version is not available (even older versions.) Thank you!

#### Geraldine_VdAuwera

Sorry @JTeer, since we no longer support older versions of GATK, we also don't provide the corresponding binaries. Perhaps you can ask colleagues if they have a copy they can share with you.

#### Geraldine_VdAuwera

Addendum: you could also download the source from the Github repository, check out the last Lite version and build from source, if you are comfortable doing that.

#### JTeer

Thanks @Geraldine_VdAuwera. The tree is a bit complex (particularly with the license changes) so I want to confirm that the following location, using the "2.3" tag is the last lite version: gatk-protected->public This seems to contain the UnifiedGenotyper (where gatk-protected->public 2.4 does not), and does not contain the HaplotypeCaller, so I think that's correct, but I don't see the Lite license, and need to confirm this is the Lite version. Thanks!

#### Geraldine_VdAuwera

@JTeer, that sounds correct, yes. If you have UG but not HC then you're ok.

Thu 17 Jan 2013

#### GATK Dev Team

###### @gatk_dev

@watsonhaigh It's not currently possible. If you explain the use case on the forum we can consider a feature request.
###### 27 Feb 17
@vibbioinfocore Thanks for having us over! Great group of participants, lots of good questions!
###### 25 Feb 17
Slides, tutorial materials from #GATK workshop in Leuven, Belgium posted at https://t.co/LaXzONIp1C
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RT @EMBL_ABR: Register your interest now in training in @gatk_dev @BroadGenomics https://t.co/gwEzuwOZYP to be run in Aus by @BioplatformsA…
###### 19 Feb 17
#GATK Support team appreciation day -- say hi and get a prize! https://t.co/J71I4FL9zA

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