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

About

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.

**Updated July 2024

Run the 'run_pipeline.sh' script to generate outputs. Assumes that possorted_bam.bam and barcodes.tsv are in the executing directory. Syntax: run_pipeline.sh samplename outdir

E.g.

./run_pipeline.sh C2_test_RAW C2_test_RAW_mgatk

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

Contact

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