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L. A. Liggett

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  • Mutect2 include MNPs

    Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. a) GATK version used 4.1.5.0b) Exact GATK commands used c) The entire error log if app...

  • Panel of Normals index files not found

    Can you please provide a) GATK version used: 4.1.5.0b) Exact GATK commands used c) The entire error log if applicable.   When running the 1-Mutect2_PON workspace, at the CreatePanel stage, some of ...

  • Stalled Shards

    Can you please provide a) GATK version used: 4.1.5.0 b) Exact GATK commands used c) The entire error log if applicable.   I am running Mutect2_PON to generate a panel of normals. Everything seems ...

  • Output files can't be found

    Can you please provide a) GATK version used: GATK4 b) Exact GATK commands used: Using v2.7.0 of the 1-Mutect2_PON walkthrough c) The entire error log if applicable.   I'm running the GATK Best Prac...