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Does the GATK read the reference from the disk frequently?
Uh..Does the GATK read the reference such as hg19 from the disk each time it runs some tools?
As the GATK will run many tools such as RealignerTargetCreator, IndelRealigner, BaseRecalibrator in a variant detection pipeline, if it read hg19 from the disk every time, it will be time-consuming...