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Geraldine Van der Auwera

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Latest activity by Geraldine Van der Auwera
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    Geraldine Van der Auwera commented,

    Hi Dr. venkateswara swamy, the syntax has changed in GATK 4 so you cannot use scripts written for earlier versions without modification. For example, this error is pointing out that the “-T” argume...

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    Geraldine Van der Auwera created an article,

    Genomics in the Cloud: Origins

    In my last blog post, I introduced the book that Brian O'Connor and I recently co-authored, Genomics in the Cloud, published by O'Reilly Media. Today I'd like to give you a more personal perspectiv...

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    Geraldine Van der Auwera created an article,

    Introducing Genomics in the Cloud, ie "The GATK book"

    I always wince a bit at the phrase "we are thrilled to announce bla bla blah" because it's such a hackneyed sentence starter. Nevertheless, I do have something to announce, and I am in fact quite t...

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    Geraldine Van der Auwera created an article,

    Detecting sample swaps with Picard tools

    By Yossi Farjoun, Associate Director of computational research methods in the Data Sciences Platform **A note to explain the context of the paper by Nauman Javed, Y.T. and others, “Detecting sample...

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    Geraldine Van der Auwera commented,

    Hi warren kretzschmar, I understand it's not ideal. Unfortunately this was necessary to reduce our maintenance burden. I would recommend that you clone the repository so that you have a local copy ...

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    Geraldine Van der Auwera commented,

    FYI our colleagues in the Genomics Platform (who do the sequencing at the Broad Institute) are presenting a poster at the AGBT meeting this week about their testing of the DRAGEN-GATK pipeline. For...

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    Geraldine Van der Auwera commented,

    MICHAEL MCMANUS Mutect2 and the somatic short variants pipeline are on the list of use cases we want to work on together, but we haven't yet decided which will be next after the germline short vari...

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    Geraldine Van der Auwera commented,

    Hi Kurt, this applies to both the single sample case and the multisample (joint calling) cases. Here we show the evaluation results from the single sample case because they're more straightforward ...

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    Geraldine Van der Auwera created an article,

    DRAGEN-GATK Update: Let's get more specific

    This post was written in collaboration with Severine Catreux (Illumina DRAGEN team), James Emery (Broad Institute GATK team) and members of the GATK support team. Last September we announced a new ...

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    Geraldine Van der Auwera commented,

    Hi David Murphy, sorry I missed your reply. I believe the team is collecting reports etc in the "Other" section of the forum here: https://gatk.broadinstitute.org/hc/en-us/community/topics/36000148...