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In GATK 1.x there was an option to discard the original quality scores for a recalibrated bam using the switch:
I think during TableRecalibration
Is there an equivalent in GATK v 2.x since as far as I can see t here is no option in PrintReads after BaseRecalibrator to discard original quality scores in favour of recalibrated quality scores.
My intention is to keep the file sizes down as much as possible