PCAWG GATK Co-cleaning workflow is developed by the Broad Institute
(https://www.broadinstitute.org), 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: https://github.com/ICGC-TCGA-PanCancer/pcawg-gatk-cocleaning.
Run the workflow with your own data
Prepare compute environment and install s
This is a companion discussion topic for the original entry at github.com/ICGC-TCGA-PanCancer/pcawg-gatk-cocleaning