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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 missing cDNA, Codon, and Protein Change for some chromosomes

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      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,

    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,

    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,

    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,

    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

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    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_...

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    Robert Bremel commented,

    Sorry, I really don't know about anything prior to 4.1.7.1 (only Docker).   I am relatively new to this whole area having spent  my career downstream in the protein world!  :-)  I only happened on ...

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    Robert Bremel commented,

    I combined the funcotator.maf files and mutect2.vcf files from 20 variant sets and tallied-up the differences. I have only been working at this for a couple of months but the issue seems to arise i...

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    Robert Bremel commented,

      I am using the docker version 4.1.8.1 vcf file ##source=FilterMutectCalls##source=Mutect2   -default command      Funcotator --output mydata/P58772/analysis/P58772_7_mutect2_funcotator_hg38.maf -...

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    Robert Bremel created a post,

    Funcotator and mutect2 coordinate system

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....