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

:Author: `Ronak H Shah <https://github.com/rhshah>`_, Donavan Cheng, `Ahmet Zehir <https://github.com/ahmetz>`_, Aijazuddin Syed, `Raghu Chandramohan <https://github.com/rghu>`_, Meera Prasad et.al
:Contact: rons.shah@gmail.com
:Source code: http://github.com/rhshah/IMPACT-Pipeline
:License: `Apache License 2.0 <http://www.apache.org/licenses/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.

.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.32716.svg
   :target: http://dx.doi.org/10.5281/zenodo.32716


Contents:

.. toctree::
   :maxdepth: 5
   
   install
   requirements
   usage
   subscripts
   filedescriptions

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 <http://www.sciencedirect.com/science/article/pii/S1525157815000458>`_.