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David Lord

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Latest activity by David Lord
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    David Lord commented,

    1. Getting Started
    2. Tutorials
    3. Funcotator Information and Tutorial

    I believe there is a typo in the README file in the v.1.7 somatic data source package. The "use case" clearly states "somatic", however, the introduction starts with: "This is a collection of data ...

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    David Lord created a post,

    Indel realignment GATK4

    Answered
    1. Community
    2. General Discussion

    Is there any way to run indel realignment on GATK4? I am aware that indel realignment is no longer necessary in the variant calling workflow of GATK4, however, I wish to perform further downstream ...

    • David Lord
    • 2 followers
    • 1 comment
    • 1 vote
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    David Lord commented,

    1. Tool Index
    2. 4.2.2.0
    3. LearnReadOrientationModel

    I'm currentlly conducting somatic variant calling through Mutect2 and I plan to use the LearnReadOrientationModel tool (my data is derived from FFPE tumor samples). Should I create the orientation ...

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    David Lord created a post,

    Perform realignment around indels before detecting MSI on BAM files?

    Answered
    1. Community
    2. General Discussion

    Greetings,  I have a set of pre-processed (duplicates marked and BQSR performed) BAM files deriving from gene-panel sequencing data. I know that realignment around indels is kind of outdated nowada...

    • David Lord
    • 4 followers
    • 2 comments
    • 0 votes