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Welcome to the wiki

The pages off to the side describe documentation and workflows for 1) genotyping mtDNA variants from sequencing data (.bam files); 2) best practices for generating .bam files; and 3) identifying high-confidence variants showing putative subclonal structure using our latest-and-greatest variant calling workflow. We've organized them below to help you get started roughly in order of utility.

Getting started

• mgatk installation
• An overview of mgatk's modes
• Enhancing mtDNA coverage in one alignment
• Genotype single-cell data from a 10x run

User configuration

• Supplying a custom mtDNA genome
• User-specified options in processing

After execution

• Understanding the main output files
• Downstream analyses in R
• Trouble shooting common errors

Large mtDNA deletions

• Vignette of identifying and quantifying heteroplasmy for large mtDNA deletions

Non-essential musings

• Thinking about circular mtDNA references