A sensitive Mitochondrial variant detection pipeline from WGS data
mity is a bioinformatic analysis pipeline designed to call mitochondrial SNV and INDEL variants from Whole Genome Sequencing (WGS) data.
- identify very low-heteroplasmy variants, even <1% heteroplasmy when there is sufficient read-depth (eg >1000x)
- filter out common artefacts that arise from high-depth sequencing
- easily integrate with existing nuclear DNA analysis pipelines (mity merge)
- provide an annotated report, designed for clinicians and researchers to interrogate
- python3 (tested on 3.7.4)
- freebayes >= 1.2.0
- bgzip + tabix
- gsort (https://github.com/brentp/gsort)
Installation instructions via Docker, pip, or manually are available in INSTALL.md
This is an example of calling variants in the Ashkenazim Trio.
mity call on three MT BAMs provided in mity/test_in.
We recommend always using
mity report won't work:
mity call \ --prefix ashkenazim \ --out-folder-path test_out \ --region MT:1-500 \ --normalise \ test_in/HG002.hs37d5.2x250.small.MT.RG.bam \ test_in/HG003.hs37d5.2x250.small.MT.RG.bam \ test_in/HG004.hs37d5.2x250.small.MT.RG.bam
This will create
test_out/normalised/ashkenazim.mity.vcf.gz (and tbi file).
We can create a
mity report on the normalised VCF:
mity report \ --prefix ashkenazim \ --min_vaf 0.01 \ --out-folder-path test_out \ test_out/ashkenazim.mity.vcf.gz
This will create:
High-depth sequencing and sensitive variant calling can create many variants with more than 2 alleles, and in some
cases, joins two nearby variants separated by shared
REF sequence into a multi-nucleotide polymorphism
as discussed in the manuscript. Here, variant normalisation relates to decomposing the multi-allelic variants and
where possible, splitting multi-nucleotide polymorphisms into their cognate smaller variants. At the time of writing,
all variant decomposition tools we used failed to propagate the metadata in a multi-allelic variant to the split
variants which caused problems when reporting the quality scores associated with each variant.
Technically you can run
mity call and
mity normalise separately, but since
mity report requires a normalised
vcf file, we recommend running
mity call --normalise.
You can merge a nuclear vcf.gz file and a mity.vcf.gz file thereby replacing the MT calls from the nuclear VCF (
presumably from a caller like HaplotypeCaller which is not able to sensitively call mitochondrial variants) with
the calls from
mity merge \ --prefix ashkenazim \ --mity_vcf test_out/ashkenazim.mity.vcf.gz \ --nuclear_vcf todo-create-example-nuclear.vcf.gz
Recommendations for interpreting the report
Assuming that you are looking for a pathogenic variant underlying a patient with a rare genetic disorder potentially caused by a Mitochondrial mutation, then we recommend the following strategy:
- tier 1 or 2 variants included in the 'commercial_panels' column
- tier 1 or 2 variants that match the clinical presentation and the phenotype in 'disease_mitomap', preferably those that are annotated with Confirmed evidence in the 'status_mitomap' column
- exclude common variants: anything linked to 'phylotree_haplotype', high 'phylotree_haplotype', high 'MGRB_frequency', high 'GenBank_frequency_mitomap'.
- consider any remaining tier 1 or 2 variants that may have a predicted impact on tRNA
- consider any remaining variants with high numbers of 'variant_references_mitomap'
- if you have analysed multiple family members, consider variants who's level of 'variant_heteroplasmy' match the disease burden
We would like to thank:
- The Kinghorn Centre for Clinical Genomics and collaborators, who helped with feedback for running
- The Genome in a Bottle consortium for providing the test data used here
- Eric Talevich who's CNVkit helped us structure
mityas a package
- Erik Garrison for developing
FreeBayesand his early feedback in optimising
FreeBayesfor sensitive variant detection.
- Brent Pederson for developing
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