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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

Can Mutect2 calls tumor sample specific SNV under joint calling mode?

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    Anthony Dias-Ciarla

    Thank you for your post, Duo Xie ! 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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    Anthony Dias-Ciarla

    Hi Duo Xie,

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

    I brought your inquiry to our developers and received some feedback to share with you.

    Firstly, the GT field in Mutect2 doesn’t mean anything; it is a historical relic that we will eventually remove. You can ignore this field. Mutect2 multi-sample mode does not make sample-specific calls but rather makes a call for the individual as a whole. If there is a call that passes after filtering, it means this mutation did exist in some part of the patient’s body at some point in time. Mutect2 is not sophisticated enough to distinguish when or in which part of the body the mutation is/was.

    I hope this helps to clarify things for you! Please let me know if you have any other questions in this regard. Thank you again for being a valued contributor to the GATK community.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Duo Xie,

    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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