User defined mtDNA reference genome

User-defined mitochondrial genome

Caleb Lareau

Several common mtDNA reference genomes are built into mgatk. If the one that you use is not present, this page shows how to supply one.

To see the supported genomes, execute the following command:

mgatk support

You'll get output that looks like this:

Mon Jan 27 14:55:58 EST 2020: mgatk v0.4.8
Mon Jan 27 14:55:58 EST 2020: List of built-in genomes supported in mgatk:
Mon Jan 27 14:55:58 EST 2020: ['GRCh37', 'GRCh38', 'GRCm38', 'GRCz10', 'NC_012920', 'hg19', 'hg19_chrM', 'hg38', 'mm10', 'mm9', 'rCRS']
Mon Jan 27 14:55:58 EST 2020: Specify one of these genomes or provide your own .fasta file with the --mito-genome flag

Providing a custom reference

Given the .fa or .fasta file that was part of your reference genome for whichever alignment tool, one can extract only the mitochondrial genome using the following command for chrM (update your mitochondrial genome name accordingly-- other examples may be MT). For example:

samtools faidx new_reference.fa chrM > new_reference_chrM.fasta

With the abridged .fasta file generated, one can supply it as the value to the --mito-genome

e.g.

mgatk bcall ... --mito-genome new_reference_chrM.fasta ...

This will import the reference genome from the user-defined fasta file, enabling the tool to work with any custom reference.