mtDNA-Server 2

mtDNA-Server 2 is based on Nextflow with the overall goal to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes.

It supports different variant callers and is able to call insertions, deletions (INDELs) and single nucleotide variants (SNVs). Furthmore it includes several modules for (a) quality control and input validation (b) haplogroup classification and contamination detection, (c) minimal VAF estimation based on the coverage to minimize false positives and (d) an interactive analytics dashboard.

Web Service

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

Documentation

Documentation can be accessed here.

Command-Line Execution with Nextflow

Requirements

• Docker or Singularity
• Java
• Nextflow

nextflow run genepi/mtdna-server-2 -r v2.1.7 -profile test,docker

Publication

Weissensteiner H*, Forer L*, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S: mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res. 44:W64-9, 2016. PMID: 27084948

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.