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Is Indel realignment removed from GATK4?

hmushtaqhmushtaq NetherlandsMember

I am seeing help of GATK4 (hellbender), and for example for the tool ReadsPipelineSpark, it says, Takes aligned reads (likely from BWA) and runs MarkDuplicates and BQSR. The final result is analysis-ready reads. In the original GATK pipeline there used to be Indel Realignment between Mark duplicates and BQSR. Is it there no more in this new version?

Best Answer


  • magicDGSmagicDGS Member

    One question regarding this is if it is possible that an independent project based on the new framework is allowed to port the code (because it have protected license). Could you help me in this regard, @Geraldine_VdAuwera?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, we hadn't thought about that but I'm sure we can find an arrangement that makes sense. Let me discuss with the team and I'll get back to you with options.

  • magicDGSmagicDGS Member

    Hello, @Geraldine_VdAuwera. Are there some advance regarding my question? Thank you in advance!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Hi @magicDGS, sorry I never got back to you! Technically the license prevents us from allowing a third party to port protected code. However at this point we are amenable to making a lot of the formerly protected code public. If you have a list of classes you'd like to port that are currently protected, we can have a look and probably switch them over. We're looking to cut one last version of GATK3 to release recent bug fixes, so this would happen in the very near future.
  • magicDGSmagicDGS Member

    Hello @Geraldine_VdAuwera, I was checking the gatk3 github repository and if I understood correctly the indel realignment pipeline is already in public. Can you confirm that?

    Although with HaplotypeCaller the indel-realignment algorithm is not necessary anymore, for Pool-Seq data it may be still important to have this feature. But because I understand that the GATK team does not need it anymore, I wonder if I can port to my own toolkit (based on the GATK4 framework) the GATK3 implementation to have a way of continuing using it. If so, the classes that I need to port are all the ones that are related with that algorithm (not the GATK engine itself, because I will use the GATK4 anyway).

    The last question is how should I license the port in my own tool. My current implementation have a MIT license, with the every class file belonging to me with the license text and my name. If the port is possible and I will maintain the code in my own public toolkit, what should I do regarding GATK? I would like to give credit to your team and the original developers, because I do not own the algorithm itself but just the port and the changes if I maintain/improve it.

    Thank you very much in advance. I'm not a lawer nor a computer scientist and I always have problems to understand how to proceed in that cases.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yes, the indel realignment classes that are in public are totally ok to port into your project, or potentially even into GATK4. As you say there are still some use cases where it may be warranted; and while we're not planning to put effort into code we no longer use, because we have to prioritize our effort toward new features, we're not opposed to taking it in if someone else is willing to do that work, in order to continue providing that functionality to the parts of the community who might still need it.

    If you choose just to port the code to your own project (which may simplify matters in case you would like to tweak the algorithm, so you don't have to depend on our approval) then you will need to keep it under the same MIT license as is currently in the code files. Here is a plain-language summary of what the MIT license stipulates, which I find quite helpful:

  • magicDGSmagicDGS Member

    Thanks for the detailed response @Geraldine_VdAuwera. I will contribute to GATK4 if the team will accept it, because it is simpler for me. If there is an algorithm tweak, I will propose a patch.

    Thank you very much for the feedback.

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