Normally these dependencies are installed automatically when running setup.py
Python 2.7 or later (https://www.python.org)
pysam (v0.8.4) (http://pysam.readthedocs.io)
pip install pysam==0.8.4
PyVCF (v0.6.8) (http://pyvcf.readthedocs.io)
pip install pyvcf==0.6.8
PyYAML (v3.11) (http://pyyaml.org)
pip install pyyaml==3.11
setuptools (v20.2.2) (https://setuptools.readthedocs.io)
pip install setuptools==20.2.2
samtools (v1 or later) (http://samtools.sourceforge.net)
apt-get install samtools
pigz (v2.3.4) (http://zlib.net/pigz)
apt-get install pigz