PCAWG GATK Co-cleaning workflow is developed by the Broad Institute
(, it consists of two pre-processing steps for tumor/normal
BAM files: indel realignment and base quality score recalibration (BQSR). The workflow
has been dockerized and packaged using CWL workflow language, the source code is available on
GitHub at:

Run the workflow with your own data

Prepare compute environment and install s

This is a companion discussion topic for the original entry at