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BaseRecalibrator/PrintReads BD and BI flags

genecgenec Member
edited January 2013 in Ask the GATK team

What are the BD and BI flags that get added to my bam files after base recalibration? They seem to consist of a long string of "N"s, and I'm trying to understand if that is correct.


Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi Gene,

    Those are insertion/deletion base qualities, where N=45, which is the default quality score for indels assigned by the BaseRecalibrator. So it looks like your reads are not getting recalibrated and are just maintaining the default original qualities.


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