CGAP Somatic Pipeline - Sentieon

This repository contains components for the CGAP pipeline for Single Nucleotide Variants (SNVs), small insertions/delitions (INDELs), and Structural Variants (SVs) in somatic data using Sentieon:

• CWL workflow descriptions
• CGAP Portal Workflow and MetaWorkflow objects
• CGAP Portal Software, FileFormat, and FileReference objects
• ECR (Docker) source files, which allow for creation of public Docker images (using docker build) or private dynamically-generated ECR images (using portal pipeline utils pipeline_deploy)

The pipeline can process analysis ready bam files for a tumor/normal comparison and produces a vcf file as output. Documentation for all CGAP Pipelines can now be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/