IndelRealigner -nWayOut specify output directory
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:
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?