1. Installation

1.1. Prerequisites

• python 3.4+

• pysam (0.11.2.2+)

• pyfaidx (0.5.3.1+)

• pytabix (0.0.2+)

• pyliftover (0.4+)

• xmltodict (0.12.0+)

• pyvcf (0.6.8+)

• tqdm (4.48.2+)

Note

If you are using pypi (pip) for MutAnno installation, you don’t need to install prerequisite python libraries because pypi can install them automatically.

1.2. Install with pypi

To install MutAnno, open a shell and run the following command:

$ pip install mutanno

1.3. Install with code from github

Alternatively, use git clone followed by setup.py

$ git clone https://github.com/dbmi-bgm/mutanno
$ cd mutanno
$ python setup.py install