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Robert Bremel

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Recent activity by Robert Bremel Sort by recent activity Recent activity Votes
  • Funcotator missing cDNA, Codon, and Protein Change for some chromosomes

    Answered

      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...

  • Mysterious Funcotator issue

    Answered

    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_...

  • 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 (....

  • Can vcf file from mutect2 be used in RNAseq short variant discovery

    Answered

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Docker gatk:latest The method suggested for RNAseq short variant discovery uses haplot...

  • mutect2 vcf header

    The  final three lines in the mutect2 header above the column headers is listed as: ##source=Mutect2##tumor_sample=N31May2020##tumor_sample=T31May2020 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ...

  • Funcotator Appears to have completed but with RunTimeException

    Can you please provide a) GATK version used  Docker 4.1.7.0b) Exact GATK commands used Funcotator -R mydata/refs/Homo_sapiens_assembly19.fasta -V mydata/P62820/analysis/P62820_mutect2_filtered.vcf ...

  • How is tumor_f in Funcotator MAF

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Using most recent GATK docker. tumor_f is not one of the columns in the MAF specificat...

  • Workaround for Missing Platform Identifier in BQSRPipelineSpark?

    I have been running the GATK best practices workflow in Docker verion 4.1.7.0 and everything was working fine up to now. BQSRPipelineSpark complained about a missing platform specifier.  It seems t...

  • MarkDuplicates and CNV bias

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. GATK Docker 4.1.7.0  I am running a "Best Practices" workflow of  tumor/normal samples...