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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Standalone HaplotypeCaller

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    Genevieve Brandt (she/her)

    Thank you for your post, Pryce Turner! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Pryce Turner

    Thank you!

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    Anthony Dias-Ciarla

    Hi Pryce Turner,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    I ran your inquiry by our developers and obtained some pertinent information for you. It is undoubtedly possible to copy and modify the code for your experimentation. We don’t know of anyone that has attempted peeling out just some minimal subset of tools to make a slimmer Docker image. You are more than welcome to try this on your own, though there is a lot of Java overhead to make things work, so you might encounter trouble pruning. So it might not be worth the effort to get a slightly smaller image?

    Additionally, this assumes that you are only doing this for research purposes. If you are looking to isolate GATK tools to create a commercial product on top of GATK, you’ll have to read our GATK license carefully.

    In summary, if it is for research purposes, you can do just about whatever you want. Still, you should clearly state that you are using your fork and not the officially maintained HaplotypeCaller in any papers produced.

    Thank you again for your contribution to the GATK forum. I hope this helps! Please do not hesitate to reach out if you have any other questions.

    Best,
    Anthony

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    Pryce Turner

    Hi Anthony,

    Thanks for following-up! I suspected as much.. without a Java background I suspect I'll be in for a pretty challenging time. Oh well - I appreciate you looking into it. 

    This is for an open-source project that's a very early prototype. I'll be sure to follow the license and any citation guidelines.

    Best,

    Pryce

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    Anthony Dias-Ciarla

    Hi Pryce Turner,

    Thank you again for your contribution to the GATK forum. As I mentioned, if you have any other questions in the future, please do not hesitate to reach out.

    I wish you luck and success!

    Best,
    Anthony

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