Installation
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
pip3 install --upgrade pip
This error results from using an old version of pip. We recommend upgrading pip
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).
