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Katherine Fawcett

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Latest activity by Katherine Fawcett
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    Katherine Fawcett commented,

    1. Community
    2. Documentation Questions
    3. DRAGEN-GATK: how to create gvcfs

    Thanks very much, James.  Do you know if this will be made part of the official DRAGEN-GATK pipeline at some point?

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    • Katherine Fawcett
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    Katherine Fawcett created a post,

    DRAGEN-GATK: how to create gvcfs

    1. Community
    2. Documentation Questions

    Hello! I would like to use the DRAGEN-GATK workflow to create a gvcfs.  When I run the workflow described here ((How to) Run germline single sample short variant discovery in DRAGEN mode – GATK (br...

    • Katherine Fawcett
    • 2 followers
    • 2 comments
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    Katherine Fawcett created a post,

    DepthOfCoverage COUNT_FRAGMENTS

    1. Community
    2. Germline

    Hi, I am using GATK 4.1.7 and would like to use DepthOfCoverage to count fragments (--countType COUNT_FRAGMENTS in the older version).  However, the current beta version of DepthOfCoverage only all...

    • Katherine Fawcett
    • 2 followers
    • 1 comment
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    Katherine Fawcett created a post,

    GermlineCNVCaller - requirements

    1. Community
    2. Germline

    Hello, I would like to use GermlineCNVCaller to identify CNVs in 10,000s of exome samples, but have a few questions before I get going: 1)  The documentation states that the memory requirements for...

    • Katherine Fawcett
    • 6 followers
    • 5 comments
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