GATK License and Redistributing in an AWS AMI

mpw6mpw6 Posts: 10Member

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?



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,326Administrator, Dev admin

    Hi there,

    I think this should be okay, but let me check with our business/legal specialist to make sure. I'll get back to you with an answer as soon as I can.

    Geraldine Van der Auwera, PhD

  • francois.sabotfrancois.sabot Montpellier, FrancePosts: 1Member

    Dear Geraldine
    We have almost the same type of question, ie our current pipelining system is using GATK, and for an easier install of the whole framework, we would like propose a running version of GATK for our tool in a embedded download.
    We were planning to add a text saying that you cannot install it if you do not respect the original GATK license (with a link to it).

    Will it be ok using such a system ?



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,326Administrator, Dev admin


    Hi Francois, we're currently working on developing a model to enable this sort of activity, and it would help to have some additional details, plus feedback on our proposed model. Would you mind discussing this with me over email? I am vdauwera at

    Geraldine Van der Auwera, PhD

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