org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Duplicate definition of argument with full name: filter_mismatching_base_and_quals

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    Root Cause Analysis

    1. org.broadinstitute.sting.utils.exceptions.ReviewedStingException

      Duplicate definition of argument with full name: filter_mismatching_base_and_quals

      at org.broadinstitute.sting.commandline.ArgumentDefinitions.add()
    2. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.commandline.ArgumentDefinitions.add(ArgumentDefinitions.java:59)
      2. org.broadinstitute.sting.commandline.ParsingEngine.addArgumentSource(ParsingEngine.java:147)
      3. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:198)
      4. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
      5. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
      5 frames