Installation

Install mgatk

Recommended: First, create a python virtual environment in some working directory to keep things tidy:

python3 -m venv venv3
source venv3/bin/activate

Next, install mgatk from PyPi:

pip3 install mgatk

This should be all that you need. To verify:

mgatk --version

Additional requirements for native execution

In addition the python mgatk package, the following R packages GenomicRanges, data.table, SummarizedExperiment, and Matrix. Note: if you specify the flag --skip-R, you can avoid the internal R execution but will have plain text enumerations of the mitochondrial genetic data.