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baserecalibrator

chenfengzhenchenfengzhen shenzhenMember

when i do baserecalibrator with my sample
i got an error "SAM/BAM/CRAM file [email protected]3dc4266 appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score (93) with BAQ correction factor of 4; please see the GATK --help documentation for options related to this error"
I tried all of the following options one by one,but it do not work.

-filterMBQ #--defaultBaseQualities 35 #--fix_misencoded_quality_scores #-fixMisencodedQuals #--allow_potentially_misencoded_quality_scores #-allowPotentiallyMisencodedQualsi

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