mtDNA-Server pipeline

mtDNA-Server specifications


Unique identifier OMICS_12341
Name mtDNA-Server
Interface Web user interface
Restrictions to use None
Input format FASTQ,BAM
Output data An interactive HTML report summarizing all findings, the detected heteroplasmic and homoplasmic sites, the HaploGrep input and final classification file and the raw pileup file including base position counts per sample.
Computer skills Basic
Version 1.0.7
Stability Stable
Maintained Yes




  • person_outline Sebastian Schönherr <>

Publication for mtDNA-Server

mtDNA-Server IN pipeline

PMCID: 5727231
PMID: 29233967
DOI: 10.1038/s41467-017-00663-9

[…] haplogrep276 was used to identify mitochondrial haplotypes for each individual. for this, all reads were aligned using bwa-mem to the rsrs sequence. the bam files produced were then uploaded to mtdna-server service as suggested by the webserver documentation. this service performs qc filtering (mapping quality score < 20; read alignment quality < 30; base quality < 20; heteroplasmy […]

mtDNA-Server institution(s)
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
mtDNA-Server funding source(s)
Supported by EU FP7 project [602133]; Austrian Science Fund (FWF) [J-3401].

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