Benchee is a SV benchmarking tool.
First you need to clone the repository:
git clone https://github.com/Joshtron/benchee
Please make sure to install pybedtools. pip and conda commands are listed below:
pip install pybedtools
conda install -c bioconda pybedtools
After successfully installing pybedtools, call the setup.py script which will enable you to use the benchee command line tool.
python /path/to/benchee_project/setup.py develop
benchee --query query.vcf --truth truth.vcf benchmark