To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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:
/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?

Best Answer

Answers

Sign In or Register to comment.