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How does ApplyBQSR handle unmapped reads?
Dear GATK team,
I am working with WGS BAM files provided by a major consortium. They applied a BWA + GATK pipeline. The quality scores were recalibrated, but the resulting BAM files do not contain an OQ tag giving the original base qualities.
What does GATK do with the base quality scores of unmapped reads in the ApplyBQSR (GATK4) or PrintReads (GATK3) tool?
My analysis involves a subset of reads drawn from mapped reads and unmapped reads. Therefore, I am concerned that this subset will contain a mixture of quality scores - recalibrated for some reads, but not for others.