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Can ApplyBQSR emit queryname sorted BAM?

calicali SydneyMember

Hi all,
I am using GATK v 4.1.2. I would like to produce queryname sorted BAM output from ApplyBQSR. The input BAM for the BaseRecalibrator step is queryname sorted. Is there a way to instruct the tool to output a specific sort order? I would very much like to avoid an additional sort step, and queryname sorting is required by the next tool in my pipeline (SAMblaster).
Thanks in advance,


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