ExScaliburGMD: Scalable and Accurate Detection of Germline Mutations from Whole Exome Sequencing in the Cloud

ExScaliburGMD is a germline mutation pipeline for Whole Exome Sequencing (WES) data developed by the Center for Research Informatics (CRI) bioinformatics core at the University of Chicago.

The pipeline is designed to be

• Scalable Manages analysis of tens to hundreds of samples
• Accurate Over 99% sensitivity and accuracy in variant detection
• Automate Full analysis pipeline from QC to annotated germline variants with submission of one master script
• Comprehensive Implements multiple aligners and callers allowing for comparison and integration of different variant sets
• Flexible Fine control of analysis modules, parameters, and environmental settings
• Robust Extensive checkpoints and error detection features
• Reproducible Quick restart of analysis and sharing of results
• Real-time Easy access and monitor of the pipeline progress
• Transferable Runs on a desktop, work station, HPC and cloud with one single switch

The pipeline is implemented in

• BigDataScript Scripting language for data pipelines
• Perl Utilities

The GMD pipeline is part of the ExScalibur suite (CRI, University of Chicago): https://exscalibur.cri.uchicago.edu.

Quick Demo#

To gain the first look into the pipelines, we provide sample data and scripts to build a small project with 3 samples.

In directory example/

• NA12878trio.metadata.txt Sample metadata table
• NA12878trio.pipeline.yaml Pipeline configuration file

The project directory myProject has been prepared for you. To regenerate the project directory and all config files in the directory, try to run

#!bash
./Build_ExScaliburGMD.NA12878trio.sh

Then the project directory will be regenerated, as well as the master job submission script Submit_ExScaliburGMD.NA12878trio.sh, which can be used to initiate the pipeline run. The full project directory structure can be viewed in myProject/NA12878trio.tree.txt.

This is a quick demo of the initialization of a project. To run real tests, please follow the instructions on ExScalibur website (https://exscalibur.cri.uchicago.edu).

Documentation

Please see the Wiki for full documentation.

Communication

For pipeline questions, please contact Riyue Bao at . For other general questions, please contact CRI bioinformatics team at .

Release

• Version 0.5.0 2015-03-31

Development

• Add checkpoints
• Add VCMM variant caller
• Add hg38 genome

More

• ExScaliburSMD somatic mutation detection
• ExScaliburViz visualization of data analysis report