CGAP Pipeline - Upstream GATK

This is the documentation for the CGAP Pipelines module for upstream processing with GATK. The pipeline components are bundled in the GitHub repository https://github.com/dbmi-bgm/cgap-pipeline-upstream-GATK.

• Overview - Upstream GATK
  • Docker Image
  • Pipeline Flow
  • Pipeline Steps
  • References
• QC - Upstream GATK
  • BAM Quality Control
• News and Updates - Upstream GATK
  • Version Updates