Whole exome processing workflow for CSI data generated by CIDR and HGSC
To run, submit the master shell script as a qsub on LOCUS as follows:
qsub -wd /path/to/existing/working/dir CSI_wes_pipeline/scripts/hgsc_batch_processing_hg19_collaborator.sh /path/to/raw/data process
to perform a dry run:
./CSI_wes_pipeline/scripts/hgsc_batch_processing_hg19_collaborator.sh /path/to/raw/data npr