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