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BaseRecalibrator and per chromosome input bam files for a lane/sample

MattBMattB NewcastleMember ✭✭

Hi I've a run my IndelRealigner stage per chromosome to speed up realignment runs as these can be quite time consuming (not via Queue) and thus have a bam file per chromosome for each lane/sample (as is discussed here http://gatkforums.broadinstitute.org/discussion/5996/ways-to-speed-up-indel-realinger), my question is: can I pass the ensemble of bam files to BaseRecalibrator with multiple -I arguments (assuming the engine will then present these files to BaseRecalibrator as a unified whole genome/lane(s)). Or will I need to merge my Indel realigned bams with Picard first into a single file before presenting these to BaseRecalibrator?

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