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PughLab pipeline suite

Installation and Dependencies

This is a collection of pipelines to be used for NGS (both DNA and RNA) analyses, from alignment to variant calling.

Start by creating a clone of the repository:

cd /path/to/some/directory
git clone https://github.com/pughlab/pipeline-suite/

Additionally, the report generation portion of this tool requires installation of the BPG plotting package for R: https://CRAN.R-project.org/package=BoutrosLab.plotting.general

Overview

DNA Pipeline

Table of contents

1. Input file format
2. Workflow (How to start a project)
3. Running individual tools
4. DNA Pipeline Output
5. Tips and Suggestions
6. Using panel of normals