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Update README.md
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B3rse authored Mar 29, 2023
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Expand Up @@ -7,7 +7,7 @@ This repository contains components for the CGAP pipeline for Single Nucleotide
* 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 [*cgap pipeline utils*](https://github.com/dbmi-bgm/cgap-pipeline-utils/) `pipeline_deploy`)
* 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*](https://github.com/dbmi-bgm/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.
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