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IndelRealigner -nWayOut specify output directory

LMYLMY ChinaMember

I'm using the GenomeAnalysisTK-3.4-0.jar version to co-realign paired tumor-normal BAMs. The -Input is set to a list file contains the paired tumor-normal BAMs directory. For example:
/pipiline-test/Normal/rmdup-realn/Normal.rmdup.bam
/pipline-test/Tumor/rmdup-realn/Tumor.rmdup.bam
And the -nWayOut is set to .realn.bam. The problem is that the output files are generated in the same folder where the shell script is in.
Is there a way I can get the output realn.bam to be in the same folder with the preview rmdup.bam?

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