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Robert Bremel

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Latest activity by Robert Bremel
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    Robert Bremel commented,

    1. Community
    2. Documentation Questions
    3. BuildBamIndex

        ./gatk BuildBamIndex --INPUT fname.bam

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    Robert Bremel created a post,

    BuildBamIndex

    1. Community
    2. Documentation Questions

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Have run this script many times previously but problem occurred with the 4.3.0 update After ...

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    • 4 comments
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    Robert Bremel commented,

    1. Community
    2. Other
    3. Does GATK4 BaseRecalibrator not understand relative paths?

    I had a similar?? issue crop up with BuildBamIndex in the docker 4.3.0.0 version on Windows 10 with WSL2 and  DockerDesktop  BuildBamIndex is supposed to only need a --INPUT argument.  It runs and ...

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    Robert Bremel commented,

    1. Getting Started
    2. Computing Platforms
    3. GATK on local HPC infrastructure

    I have been using the GATK Docker image with Docker Desktop on a Windows workstation and it works fine.  As a bit of a displacement activity while I am dodging delta I am thinking about building a ...

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    Robert Bremel created a post,

    Funcotator missing cDNA, Codon, and Protein Change for some chromosomes

    Answered
    1. Community
    2. Other

      I am using the :latest  docker version of GATK, running on Docker Desktop on a high-end Windows 10 workstation with 128GB RAM I had a strange occurrence that seems to be a glitch in the system so...

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    Robert Bremel commented,

    1. Getting Started
    2. FAQ
    3. FAQ for Mutect2

    Hi, I had a strange occurrence that seems to be a glitch in the system somewhere.  A week or so ago I had something crop up with Funcotator which led me to install v1.7 of the source materials.  I ...

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    Robert Bremel commented,

    1. Community
    2. Somatic
    3. Mysterious Funcotator issue

    Hi, I copied it from the Funcotator webpage,  Just to be clear -- I am running the Docker version in Docker Desktop on a Windows 10 workstation.  The workstation has 128 GB memory and I believe Doc...

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    Robert Bremel commented,

    1. Community
    2. Somatic
    3. Mysterious Funcotator issue

    Thanks again Genevieve, I think I have stashed the offending lines somewhere I will see if I can find them.  It was a really unusual indel with three TLOD values each of which was mapping perhaps a...

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    Robert Bremel commented,

    1. Community
    2. Somatic
    3. Mysterious Funcotator issue

    Thanks Genevieve,  I will download and install the 1.7 data sources.  I thought I was really up to date using 1.6 as 1.2 is in your examples.  I found a workaround that I could remove two lines fro...

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    Robert Bremel created a post,

    Mysterious Funcotator issue

    Answered
    1. Community
    2. Somatic

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: Docker 4.2.0 b) Exact command used: ./gatk Funcotator -R mydata/refs/Homo_sapiens_assembly38.fasta -V mydata/PAAD_00034_...

    • Robert Bremel
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    • 8 comments
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