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.
The documentation can be accessed here.
git clone github.com/genepi/mtdna-server-2
nextflow run main.nf -c tests/test_single_bam.config -profile docker
You can find all additional DSL2 parameters and configuration options here.
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. 52:W102-W107, 2024. PMID: 38709886
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.