.. iCallSV documentation master file, created by
   sphinx-quickstart on Mon Jun  6 11:08:33 2016.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

iCallSV: Structural Aberration Detection from NGS datasets
================================================================

:Author: Ronak H Shah
:Contact: rons.shah@gmail.com
:Source code: http://github.com/rhshah/iCallSV
:Wiki: http://icallsv.readthedocs.io/en/latest/
:License: `Apache License 2.0 <http://www.apache.org/licenses/LICENSE-2.0>`_

.. image:: https://landscape.io/github/rhshah/iCallSV/master/landscape.svg?style=flat
   :target: https://landscape.io/github/rhshah/iCallSV/master
   :alt: Code Health
   

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.184864.svg
	:target: https://doi.org/10.5281/zenodo.184864
   

.. image:: https://codecov.io/gh/rhshah/iCallSV/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/rhshah/iCallSV
   


iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. 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
========

We are in the process of publishing a manuscript describing iCallSV as part of the Structural Variant Detection framework.
If you use this software in a publication, for now, please cite our website `iCallSV <http://github.com/rhshah/iCallSV>`_.

Contents:

.. toctree::
   :maxdepth: 4

   iCallSV


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

