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Discard original quality scores after recalibration in GATK v2

cbuxtoncbuxton Posts: 2Member

In GATK 1.x there was an option to discard the original quality scores for a recalibrated bam using the switch:
--doNotWriteOriginalQuals
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
Thanks

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  • cbuxtoncbuxton Posts: 2Member

    ah, that is very helpful, makes sense to do it that way around, Thanks

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