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David Benjamin

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Latest activity by David Benjamin
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    David Benjamin commented,

    1. Community
    2. Somatic
    3. Mutect2 - Joint calling

    Joe Doasi You may also use multisample mode with a time series.  The important thing is that all samples must come from the same person: multiple sites of one tumor, time series, primary tumor and ...

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    David Benjamin commented,

    1. Community
    2. Documentation Questions
    3. Germline sites in Mutect2

    G E Turning on -genotype-gemline-sites should not affect downstream filtering, but unfortunately I neglected to exclude germline sites from the clustered events filter, and so turning on this argum...

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    David Benjamin commented,

    1. Community
    2. Somatic
    3. Mutect2 genotype-germline-sites filtering discrepancy

    TA The issue with the clustered events and haplotype filters when running in -genotype-germline-sites is a real problem.  These filters should only be triggered by a cluster of technical artifacts ...

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    David Benjamin commented,

    1. Community
    2. Documentation Questions
    3. mutect2 multi-sample

    Alessio Locallo   My question is: should I use the PON when I run Mutect2 in multi-sample as well? Or is the PON not necessary when running Mutect2 in multi-sample mode? You should still use a pa...

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    David Benjamin commented,

    1. Community
    2. Documentation Questions
    3. mutect2 multi-sample

    D the -normal argument specifies the normal samples; all others are presumed to be tumor samples.

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    David Benjamin commented,

    1. Community
    2. Documentation Questions
    3. Mutect2 panel of normals design

    Before answering your questions, we need to point out a few things: The panel of normals' role is only to clean technical artifacts, not remove germline mutations, which is handled by the germline...

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    David Benjamin commented,

    1. Community
    2. Somatic
    3. Germline false positives in Mutect2

    You have to specify -normal to tell Mutect2 which sample is the normal.  You may exclude -tumor-sample.

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    David Benjamin commented,

    1. Community
    2. Somatic
    3. Germline false positives in Mutect2

    Just -normal-sample, and keep your other arguments the same.  And you can continue to specify -tumor-sample if it's a hassle to change all your scripts, but it has no effect.

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    David Benjamin commented,

    1. Community
    2. Somatic
    3. Germline false positives in Mutect2

    TMB You are inadvertently running in multi-sample mode: Mutect2 thinks both samples are tumors.  You need to specify -normal-sample, and -tumor-sample is a deprecated optional argument (it does not...

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    David Benjamin commented,

    1. Community
    2. Somatic
    3. strand_bias filtering is never emitted

    G E We studied those particular Novaseq artifacts extensively a couple years ago and also informed Illumina, and found the read orientation filter to be effective.  Your data show some questionable...