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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

What does RAW_MQ annotation mean ?

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    Genevieve Brandt (she/her)

    Thank you for your post, Robert Baldwin! 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 Robert Baldwin,

    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, would you be able to clarify how exactly you created your VCF? It would be helpful if you try checking inside the header of the VCF for all of the commands you have run on the file so far. Once you locate this, please include it in your response to this post, and we can move forward with diagnosing the problem.

    It might look something like this:

    ##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.4-46-gbc02625,Date="Fri Sep 25 10:45:27 EDT 2015",Epoch=1443192327688,CommandLineOptions="analysis

    I hope to hear back from you soon! Please include any further questions that may arise in your response.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Robert Baldwin,

    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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