mtDNA-Server protocols

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mtDNA-Server specifications

Information


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

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Documentation


Maintainer


  • person_outline Sebastian Schönherr <>

Publication for mtDNA-Server

mtDNA-Server in pipeline

2017
PMCID: 5727231
PMID: 29233967
DOI: 10.1038/s41467-017-00663-9

[…] haplogrep2 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 […]


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mtDNA-Server in publications

 (4)
PMCID: 5837733
PMID: 28444229
DOI: 10.1093/eurheartj/ehx174

[…] of ngs reads. data analysis was therefore performed by aligning all reads to one single kringle repeat and low-level variants were called using the highly specific mutation detection pipeline ‘mtdna-server’ with slight adaptions (https://mtdna-server.uibk.ac.at/, 25 march 2017) (see ). the lpa kiv-2 specific variant calling pipeline will be available at lpa-server.i-med.ac.at, 25 march […]

PMCID: 5334155
PMID: 28244283
DOI: 10.3346/jkms.2017.32.4.587

[…] haplogrep2 (25; http://haplogrep.uibk.ac.at) according to the phylotree build 16 database (26; van oven et al. 2009). mtdna mps raw data in binary alignment/map (bam) format were also loaded on the mtdna-server (27; available at http://mtdna-server.uibk.ac.at) in order to investigate the heteroplasmic variants and confirm the data quality., this study was approved by the ethical committee […]

PMCID: 4539931
PMID: 26282399
DOI: 10.1186/s13062-015-0071-8

[…] research group databases and information systems (dbis) at the university of innsbruck exists, developing data-intensive bioinformatics software solutions such as cloudgene [], haplogrep [] or the mtdna-server (http://mtdna-server.uibk.ac.at). lately, the developed workflow system cloudgene has been utilized as the underlying architecture for the michigan imputation server, developed […]

PMCID: 4532422
PMID: 26262956
DOI: 10.1371/journal.pone.0135643

[…] well as the two original dna samples, we were able to exactly quantify the minor components at the 1% level as obtained from the 1+99 mixture by lowering the detection threshold to 0.8% within the mtdna-server application. position 16189 was not found at the 1% level. however, we found three additional mutations at 9462, 15236 and 16129, which were confirmed as private heteroplasmic mutations […]


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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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