variant-tools 3.1.1

Variant tools: an integrated annotation and analysis package for next-generation sequencing data

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 might need to install

• libboost
• gsl
• numpy
• Cython
• A C++ compiler such as gcc

and re-run the command if there is no binary (wheel) distribution for your platform.

Finally, you can checkout the latest version of variant tools from github, and install it with command

python setup.py install

with the aforementioned packages installed.

Documentation

Please refer to Variant Tools documentation for details.