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  • GATK: -I parameter in RealignerTargetCreator

    Hello all,

    I trying to run GATK RealignerTargetCreator prior to the IndelRealigner.

    The RealignerTargetCreator takes as the -I parameter a sample BAM file. Does anybody know what does the sample BAM file is for? Can I use a generic file for all the analyses?

    any help will be apprecited.

    Thanks
    Jorge

  • #2
    As far as I know the -I Argument is your input BAM file...

    Comment


    • #3
      Ok Thanks,

      I'll use my input bam file

      Jorge

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