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

:Author: `<NAME> <https://github.com/rhshah>`_, <NAME>, `<NAME> <https://github.com/ahmetz>`_, <NAME>, `<NAME> <https://github.com/rghu>`_, <NAME> et.al
:Contact: <EMAIL>
: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.

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>`_.

Requirements
============

Please See template.conf file in the configuration folder.

:perl: `v5.20.2 <http://perl5.git.perl.org/perl.git/tag/2c93aff028f866699beb26e5e7504e531c31b284>`_
:python: `v2.7.8 <https://www.python.org/download/releases/2.7.8/>`_
:R: `v3.1.2 <http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz>`_

Tools Used
==========
:Somatic SNV calling: `MuTect v1.1.4 <https://github.com/broadinstitute/mutect/tree/1.1.4>`_
:Somatic INDEL calling: `SomaticIndelDetector GATK v2.3-9 <http://www.broadinstitute.org/gatk/download>`_
:Somatic INDEL calling: `PINDEL v0.2.5a7 <https://github.com/genome/pindel/tree/v0.2.5a7>`_
:Somatic Structural Variant Framework: `IMPACT-SV v1.0.1 <https://github.com/rhshah/IMPACT-SV/tree/1.0.1>`_

Usage
=====
**RunIlluminaProcess.pl [options]**
	--config|c                        S Path to configration file(required)
	--svConfig|sc                     S Path to structural variant configration file(optional)
	--symLinkFlag|sf           	   I Flag for Keeping or removing the symolic links(1:Remove;2:Keep)(default:2)
	--dataDirectory|d                 S Path where all the files to be processed are located (required)
	--outputDirectory|o               S Path where all the output files will be written (required)<commit_msg>README CHANGES<commit_after>IMPACT-Pipeline: MSK-IMPACT assay data analysis framework to process data on LSF/SGE
====================================================================================

:Author: `<NAME> <https://github.com/rhshah>`_, <NAME>, `<NAME> <https://github.com/ahmetz>`_, <NAME>, `<NAME> <https://github.com/rghu>`_, <NAME> et.al
:Contact: <EMAIL>
: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.

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>`_.

Requirements
============

Please See template.conf file in the configuration folder.

:perl: `v5.20.2 <http://perl5.git.perl.org/perl.git/tag/2c93aff028f866699beb26e5e7504e531c31b284>`_
:python: `v2.7.8 <https://www.python.org/download/releases/2.7.8/>`_
:R: `v3.1.2 <http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz>`_

Tools Used
==========
:Somatic SNV calling: `MuTect v1.1.4 <https://github.com/broadinstitute/mutect/tree/1.1.4>`_
:Somatic INDEL calling: `SomaticIndelDetector GATK v2.3-9 <http://www.broadinstitute.org/gatk/download>`_
:Somatic INDEL calling: `PINDEL v0.2.5a7 <https://github.com/genome/pindel/tree/v0.2.5a7>`_
:Somatic Structural Variant Framework: `IMPACT-SV v1.0.1 <https://github.com/rhshah/IMPACT-SV/tree/1.0.1>`_

Usage
=====
**RunIlluminaProcess.pl [options]**
	
	--config|c                        S Path to configration file(required)
	
	--svConfig|sc                     S Path to structural variant configration file(optional)
	
	--symLinkFlag|sf           	   I Flag for Keeping or removing the symolic links(1:Remove;2:Keep)(default:2)
	
	--dataDirectory|d                 S Path where all the files to be processed are located (required)
	
	--outputDirectory|o               S Path where all the output files will be written (required)
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