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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

GATK HaplotypeCaller issues with Genotyping (GT)

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    Genevieve Brandt (she/her)

    Thank you for your post, pb! I want to let you know we have received your question and will be moving it to the Community Discussions -> Special GATK Use Cases topic, as the Other topic is for reporting bugs and issues with GATK.

    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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    Anthony DiCi

    Hi pb,

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

    I brought your inquiry to our development team and received feedback and clarifying questions that I'd like to share.

    Firstly, please clarify what you believe the truth to be in your second run with the "--recover-all-dangling-branches" option enabled and why? 

    Are you convinced the second site you referenced has a verifiable, easily-identifiable variant that HaplotypeCaller is missing? If yes, please provide a snippet of your bam file so that the developers can attempt to debug it. Unfortunately, they can't dig deeper into this issue without more information.

    I hope to hear back from you soon! Thank you in advance for any further information and clarity you can provide.

    Best,
    Anthony

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    Anthony DiCi

    Hi pb,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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