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

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Variant Tools

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


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.


Please refer to Variant Tools documentation for details.

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