Metadata-Version: 2.1
Name: variant_tools
Version: 3.1.3
Summary: Variant tools: an integrated annotation and analysis package for next-generation sequencing data
Home-page: http://varianttools.sourceforge.net
Author: Bo Peng
Author-email: bpeng@mdanderson.org
Maintainer: Bo Peng
Maintainer-email: varianttools-devel@lists.sourceforge.net
License: GPL3
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pyzmq
Requires-Dist: tables
Requires-Dist: numpy
Requires-Dist: Cython
Requires-Dist: scipy
Requires-Dist: pycurl

[![PyPI version](https://badge.fury.io/py/variant-tools.svg)](https://badge.fury.io/py/variant-tools)

# Variant Tools

A command line tool for the manipulation, annotation, and analysis of genetic variants
from next-generation sequencing studies.

# Installation

If you are using a conda environment, you can install variant tools with command

```
conda install variant_tools -c bioconda -c conda-forge
```
Option `-c conda-forge` is required to enforce the use of `conda-forge` version of dependencies (e.g. `boost-cpp`) over their counterpoarts in the base channel.

Otherwise, you can try to install it through `pip`

```
pip install variant_tools
```

You will need to install

* `libboost`
* `gsl`
* `numpy`
* `Cython`
* `hdf5`
* `blosc`
* A C++ compiler such as `gcc`

which, in a conda environment, could be installed with command

```
conda install -c conda-forge boost-cpp gsl numpy cython blosc hdf5
```

This method can be used if you download or clone the latest version
of variant tools from this repository.

# Documentation

Please refer to [Variant Tools documentation](https://vatlab.github.io/vat-docs/) for details.
