CGAP Pipeline for Somatic Single Nucleotide Variants and small INDELs

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

• 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 starts from tumor/normal vcf files and produces filtered and annotated vcf files containing SNVs and small INDELs as output. It also prioritizes and annotates putative driver mutations applying the decision tree developed by Hartwig Medical Foundation. Documentation for all CGAP Pipelines can now be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/