The current GATK version is 3.7-0
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1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

GATK License and Redistributing in an AWS AMI

mpw6mpw6 Member Posts: 10

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?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,651 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, FranceMember Posts: 1

    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 ?

    Cheers

    Francois

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin

    @francois.sabot

    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 broadinstitute.org

    Geraldine Van der Auwera, PhD

  • rrtrrt Member Posts: 2

    Dear Geraldine,

    Do you have any update on this question?

    Some what related, do you know any GATK based cloud platform which also includes the modules from Broad's Genepattern?

    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin

    Hi @rrt,

    Since there are actually two rather different questions addressed in this thread I'll give an update on both. In both cases, if you'd like to follow up or discuss in more detail, please email me with the details of your use case and I'll see what we can do to enable you to achieve your goal.

    Cloud platforms / BYOL

    Providing GATK analysis as a service on the cloud is not currently allowed but the situation is evolving rapidly and I hope to be able to give a more positive answer in the near future.

    Downloadable docker or equivalent for on-premises execution

    At this time we don't have a blanket policy in place, but we are able to grant individual requests to bundle GATK into a research pipeline on a case by case basis.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin

    Regarding your other question, I'm not aware of any existing options, aside from a pilot project that we are running called FireCloud that includes GATK and other Broad cancer genome analysis tools. It's not yet accessible to researchers outside Broad due to pending regulatory approval, but the plan is to open it up to the general community. I can't guarantee that it will have everything GenePattern currently includes, but there is a feature for users to add tools.

    Geraldine Van der Auwera, PhD

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