Is it OK to stack IndelRealigner runs

Hi GATK Team,

My question is related to whether it is OK to run IndelRealigner twice on the same .bam file, first individually, and next with its tumor or normal pair. This seems to be what's recommended in the PPT on the google drive titled "Somatic Variant Discovery"
https://drive.google.com/a/case.edu/folderview?id=0BwTg3aXzGxEDVk5RcEF3WW1SQWM&usp=sharing#

but I wanted to double-check because I also read that IR modifies the mapping quality of reads that it realigns, which might affect the next IR run. Any insight would be much appreciated. Thanks so much.

Sincerely,
Steve

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