simexin / IMPACT-SV

Detection of Structural Variants Using Delly and Annotation using dRanger

NOTE:

This code base is deprecated, thus it will be no longer maintained, we have a newer and much better version to do structural variant calling which is available here: iCallSV

IMPACT-SV: MSK-IMPACT assay data analysis framework to Detect/Annotate structural abberation using LSF/SGE

Author:	Ronak H Shah
Source code:	http://github.com/rhshah/IMPACT-SV
License:	Apache License 2.0

IMPACT-SV is a Perl/Python command-line software toolkit to process data, call somatic structural aberrations (SV) 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.

as well for code cite:

Requirements

Please See template.conf file in the configuration folder.

perl:	v5.20.2
python:	v2.7.8

Tools Used

Somatic Structural Variant Calling:	DELLY v0.6.1