mtDNA-Server 2

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.

Version History

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.

Are your files not working?

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.

How to execute mtDNA-Server 2?

mtDNA-Server 2 is available as a hosted web-service at the Medical University of Innsbruck or as a Nextflow pipeline.

Web Service

mtDNA-Server 2 is hosted as a free service on our mitoverse platform.

Documentation

The web-service documentation can be accessed here.

Nextflow Pipeline

To run mtDNA-Server 2 via Nextflow, please execute the following steps.

Quick Start

Install Nextflow (>=22.10.4)
Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm.
```
nextflow run genepi/mtdna-server-2 -r v2.1.14 -profile test,<docker,singularity,slurm>
```
Run Pipeline on own data

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 v2.1.14 -c <your-config-file> -profile <docker,singularity,slurm>
```

Parameters

The following parameters can be set in the configuration file.	Parameter	Default Value
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
output	null	Specific Output folder

Development

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