Skip to content

Latest commit

 

History

History
86 lines (60 loc) · 4.23 KB

README.md

File metadata and controls

86 lines (60 loc) · 4.23 KB
Raw

mtDNA-Server 2

mtdna-server-2 nf-test

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.

image

Version History

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

  1. Install Nextflow (>=22.10.4)

  2. Run the pipeline on our test dataset and select either Docker, Singluarity or Slurm.

nextflow run genepi/mtdna-server-2 -r v2.1.11 -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 v2.1.11 -c <your-config-file> -profile docker

Parameters

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
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

Publication

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.

Contact

This software was developed at the Institute of Genetic Epidemiology, Medical University of Innsbruck

Sebastian Schoenherr (@seppinho)

Hansi Weissensteiner (@whansi)

Lukas Forer (@lukfor)

License

MIT Licensed.