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Recent activity by MPetlj Sort by recent activity Recent activity Votes
  • Mutect errors

    Hello,  I used Mutect2 Terra workflow to successfully call mutations in 232/241 samples.  Mutect2 version: mutect2: JobID: 45b78f7b-c418-47b5-bc64-f729602e6679 JobHistory: https://app.terra....

  • Funcotator errors

    Hello, I am trying to use the Funcotator workflow in Terra https://dockstore.org/workflows/github.com/broadinstitute/gatk/Funcotator: To annotate a VCF that was produced by the Mutect2_pon w...

  • Mutect2 output - resources?

    Hello, I recently ran mutect2: workflow in Terra. I was wondering what is the best resource to read about the various output files produced, as well as the filtering strategies used to gener...

  • Mutect2-PON Storage object issue when running across multiple samples?

    GATK version used  : Hello, I am getting the following error when running the Mutect2_pon workflow across multiple samples (but the same worflow ran successfully over 2 samples):   Failed t...

  • Mutect2 Funcotator error

    Hi,    I am trying to run Mutect2 (github.com/broadinstitute/gatk/mutect2: workflow in Terra, but it seems to be failing at Funcotator because annotated.maf.idx file is not being created? I...

  • Mutect2 PON - gnomAD input?

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. I am trying to run Mutect2 PON workflow (https://portal.firecloud.org/?return=terra#me...