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Robert Bremel

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Latest activity by Robert Bremel
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    Robert Bremel created a post,

    Funcotator problem

    1. Community
    2. Other

    I started two Docker containers of Funcotator this morning and they both crashed in about the same place.   I had started them earlier but they seemed to have finished quicker than they should have...

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    Robert Bremel commented,

    1. Community
    2. Other
    3. string length error generated by funcotator while processing a mutect2 vcf

    Hi, What exactly is a "known edge case"? I've used 1.7  for quite a while without problems.  The link given on the resource-bundle site does not have 1.8.  The link seems to date to 2016?  I got 1....

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    Robert Bremel commented,

    1. Community
    2. Other
    3. string length error generated by funcotator while processing a mutect2 vcf

    The problem is that I can not figure out what line is the problem.  chr12 98601528  is the last line in the funcotator .maf.  Funcotator seems to grab a number of lines at a time while it is workin...

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    Robert Bremel created a post,

    string length error generated by funcotator while processing a mutect2 vcf

    1. Community
    2. Other

    A string length error is generated by functator while processing a vcf from mutect2.   java.lang.StringIndexOutOfBoundsException: begin 1086, end 1089, length 1086  (more below) funcotator stops a...

    • Robert Bremel
    • 2 followers
    • 5 comments
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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 ...

    • Robert Bremel
    • 2 followers
    • 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

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    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...

    • Robert Bremel
    • 2 followers
    • 1 comment
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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 ...