Filter out reads that do not have an original quality quality score (OQ) tag

Category Read Filters


The OQ tag can be added during the base recalibration process in order to preserve original information.

Usage example

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf NoOriginalQualityScores

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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.