!DANGER!

This codebase is deprected and is no maintained/used in its current form.

IMPACT-Pipeline: MSK-IMPACT assay data analysis framework to process data on LSF/SGE

Author:	Ronak H Shah, Donavan Cheng, Ahmet Zehir, Aijazuddin Syed, Raghu Chandramohan, Meera Prasad et.al
Contact:	rons.shah@gmail.com
Source code:	http://github.com/rhshah/IMPACT-Pipeline
Wiki:	http://impact-pipeline.readthedocs.org/en/latest/index.html
License:	Apache License 2.0

IMPACT-Pipeline is a Perl/Python/R command-line software toolkit to process data, call somatic aberrations (SNV,INDELS,SV,CNV) generated by NGS based MSK-IMPACT assay. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina.

For Description/Usage/Help:

Please visit here: IMPACT-Pipeline Wiki

Citation

If you use this software in a publication, please cite our paper

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.

for code citation use: