MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

Bioinformatics. 2014 Nov 1;30(21):3115-7. doi: 10.1093/bioinformatics/btu483. Epub 2014 Jul 14.


Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.

Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.

Availability and implementation: MToolBox package is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Mitochondrial / chemistry*
  • Genetic Variation*
  • Genome, Mitochondrial*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Molecular Sequence Annotation
  • Sequence Analysis, DNA / methods*
  • Software*


  • DNA, Mitochondrial