mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes, details can be found in our NAR publication.
Release v2.1.15 - Add option for min mean coverage
Release v2.1.14 - Load resource conf
Release v2.1.13 - Update to latest Haplogrep3
Release v2.1.12 - Install Haplogrep3 tree directly.
Release v2.1.11 - Improve QC command, update to latest mutserve v2.0.1.
Release v2.1.10 - Improved mutect2 support: create missing RG tags, write inidividual reference sequence on the fly, support complex ref tags.
We want to steadily improve mtDNA-Server 2. If your files are not working, please feel free to create a issue or contact [Sebastian] directly.
mtDNA-Server 2 is available as a hosted web-service at the Medical University of Innsbruck or as a Nextflow pipeline.
mtDNA-Server 2 is hosted as a free service on our mitoverse platform.
The web-service documentation can be accessed here.
To run mtDNA-Server 2 via Nextflow, please execute the following steps.
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Install Nextflow (>=22.10.4)
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Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm.
nextflow run genepi/mtdna-server-2 -r v2.X.XX -profile test,<docker,singularity,slurm>
To run mtDNA-Server 2 on your own data, create a config file and run the following command:
nextflow run genepi/mtdna-server-2 -r v2.X.XX -c <your-config-file> -profile <docker,singularity,slurm>
The following parameters can be set in the configuration file.
| Parameter | Default Value | Comment |
|---|---|---|
| project | null | Project name (required) |
| files | null | Input BAM files (required) |
| mode | fusion | Mode of operation (mutserve,mutect2,fusion) |
| detection_limit | 0.02 | Detection limit for heteroplasmic sites |
| coverage_estimation | on | Coverage estimation enabled |
| subsampling | off | Subsampling on/off |
| subsampling_coverage | 2000 | Subsampling coverage |
| mapQ | 20 | Mapping quality threshold |
| baseQ | 20 | Base quality threshold |
| alignQ | 30 | Alignment quality threshold |
| min_mean_coverage | 50 | Min Mean coverage |
| output | null | Specific Output folder |
git clone https://github.com/genepi/mtdna-server-2
cd mtdna-server-2
docker build -t genepi/mtdna-server-2 . # don't ignore the dot
nextflow run main.nf -profile test,development
Weissensteiner H*, Forer L*, Kronenberg F, Schönherr S. mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics. Nucleic Acids Res. 2024 May 6:gkae296. doi: 10.1093/nar/gkae296. Epub ahead of print. PMID: 38709886.
This software was developed at the Institute of Genetic Epidemiology, Medical University of Innsbruck
MIT Licensed.