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Base recalibration error with miscoded quality score >70

mavershangmavershang Austin,TxMember
edited October 2014 in Ask the GATK team

Hi, I am using GATK 3.2.2 to do base recalibration, and added --allow_potentially_misencoded_quality_scores. However, the process fails with error "we encounter
ed an extremely high quality score (71) with BAQ correction factor of 4".

It seems --fix_misencoded_quality_scores could help it process without poping error, but I am not sure if that is the correct solution.

Thanks.

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