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

Common error messages in installation

PEP 517 Error

Building wheels for collected packages: numpy, pandas, pyyaml, datrie, pyrsistent
Building wheel for XXXXX (PEP 517) ... error
ERROR: Command errored out with exit status 1
...

This error results from using an old version of pip. We recommend upgrading pip:

pip3 install --upgrade pip

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.

We utilize Picard tools for PCR duplicate removal. Thus, java is by default a required dependency. While not recommended, you can avoid this dependency by throwing the --keep-duplicates flag, which will circumvent the java call (but retain likely PCR duplicates, which we've found decreases the interpretability of variants by introducing additional false positives).