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L. A. Liggett

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Latest activity by L. A. Liggett
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    L. A. Liggett commented,

    1. Community
    2. Somatic
    3. Mutect2 include MNPs

    Bhanu Gandham it looks like this error can be solved by passing `--max-mnp-distance 0` when building the panel of normals. However, this option is not available in the best practices workflow that ...

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    L. A. Liggett commented,

    1. Community
    2. Somatic
    3. Mutect2 include MNPs

    Thanks Bhanu Gandham, I did upload (named `liggett_3_12_20.zip`) the vcf and index with the error log since it looks to me that the error is in processing chr10:60784794 from the vcf. Does this wor...

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    L. A. Liggett created a post,

    Mutect2 include MNPs

    1. Community
    2. Somatic

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. a) GATK version used 4.1.5.0b) Exact GATK commands used c) The entire error log if app...

    • L. A. Liggett
    • 2 followers
    • 5 comments
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    L. A. Liggett created a post,

    Panel of Normals index files not found

    1. Community
    2. Somatic

    Can you please provide a) GATK version used: 4.1.5.0b) Exact GATK commands used c) The entire error log if applicable.   When running the 1-Mutect2_PON workspace, at the CreatePanel stage, some of ...

    • L. A. Liggett
    • 2 followers
    • 1 comment
    • 0 votes
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    L. A. Liggett created a post,

    Stalled Shards

    1. Community
    2. Somatic

    Can you please provide a) GATK version used: 4.1.5.0 b) Exact GATK commands used c) The entire error log if applicable.   I am running Mutect2_PON to generate a panel of normals. Everything seems ...

    • L. A. Liggett
    • 2 followers
    • 1 comment
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    L. A. Liggett commented,

    1. Community
    2. Somatic
    3. Output files can't be found

    David Benjamin This seems to have fixed the issue. The job has been running for 2.5 hours at this point so hopefully works. Thanks.

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    L. A. Liggett commented,

    1. Community
    2. Somatic
    3. Output files can't be found

    David Benjamin I am running the WDL, not an associated jupyter notebook. And I am setting the gatk_docker to `workspace.gatk_docker`. And the field isn't suggesting an input for the 4.1.5.0 docker;...

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    L. A. Liggett commented,

    1. Community
    2. Somatic
    3. Output files can't be found

    David Benjamin It looks like the workspace I'm using was updated to 4.1.4.1. And I'm using v2.7.0 of the Mutect2_PON, but I do not see any way of adjusting the GATK version. Is this something that ...

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    L. A. Liggett created a post,

    Output files can't be found

    1. Community
    2. Somatic

    Can you please provide a) GATK version used: GATK4 b) Exact GATK commands used: Using v2.7.0 of the 1-Mutect2_PON walkthrough c) The entire error log if applicable.   I'm running the GATK Best Prac...

    • L. A. Liggett
    • 2 followers
    • 6 comments
    • 0 votes