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-allowPotentiallyMisencodedQuals flag did not work for BaseRecalibrator

-allowPotentiallyMisencodedQuals works well with IndelRealigner. But when using it with BaseRecalibrator, it still complains the extremely high quality scores.

ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8): 
##### ERROR
#### ERROR MESSAGE: SAM/BAM file SAMFileReader{/data004/GIF_1/GIF_1/lwang/./bam/RIMMA0468_Andean.IndelRealigned.bam} appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score (68) with BAQ correction factor of 4; please see the GATK --help documentation for options related to this error

Any suggestions? GATK version 3.1 is used here. Thanks!

Best Answer

Answers

  • fernfern Member

    Gotcha, I used the default arguments in BaseRecalibrator, did not know if the baq flag is off or not. By using the fixing the score flag, it gets working now.

    Thanks!

    Li

  • huangjianhuangjian chinaMember

    Hi,fern.I met same question when i run BaseRecalibrator. I add -fixMisencodedQuals into arguments then i got through this.But i m wondering if you deal with the question using the same argument.

  • fernfern Member

    @huangjian said:
    Hi,fern.I met same question when i run BaseRecalibrator. I add -fixMisencodedQuals into arguments then i got through this.But i m wondering if you deal with the question using the same argument.

    yes, exactly

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