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Source code is made freely available and a packaged install version is provided through PyPi.

This repository houses the mgatk package, a python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

Check out the mgatk documentation for more information and user guides.

The mgatk package was developed and is maintained by Caleb Lareau.