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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

Picard CollectHsMetrics output

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    Genevieve Brandt (she/her)

    Thank you for your post, Giovanni Cerchia! 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 Giovanni Cerchia,

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

    I brought this to our developers for some input and received some feedback. They helped me identify the location in the code where the calculations you reference take place.

    TargetMetricsCollector (Picard) - Line 617

    I hope this helps! If you have any further questions about the CollectHsMetrics tool or any others, please do not hesitate to reach out.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Giovanni Cerchia,

    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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