Attention:
The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

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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