ExScaliburSMD: Scalable and Accurate Detection of Somatic Mutations from Whole Exome Sequencing in the Cloud

ExScaliburSMD is a somatic mutation pipeline for whole-exome sequencing data developed by the Center for Research Informatics at the University of Chicago. It is designed to be flexible, robust, and to take advantage of multiple alignment and variant-calling algorithms.

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 somatic 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
• Python Utilities

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

Documentation

Please see the Wiki for full documentation.

Communication

For pipeline questions, please contact Kyle Hernandez (kmhernan at uchicago dot edu). For other general questions, please contact the CRI bioinformatics team (bioinformatics at bsd dot uchicago dot edu).

Release

• Version 0.5.0 2015-03-31
• Version 0.5.1 2015-08-31 - migrating the wiki from bitbucket to github

Development

• Add checkpoints
• Add hg38 genome

More

• ExScaliburGMD germline detection
• ExScaliburViz visualization of data analysis report