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

Abstract

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 https://sourceforge.net/projects/mtoolbox/.

Fig. 1.

The main steps of the MToolBox workflow: (a–d) read mapping and NumtS filtering; (e–h) post-mapping processing; (i–m) genome assembly, haplogroup prediction and variant annotation. In brackets, programs or modules particularly important for the associated process. Solid connectors indicate mandatory pipeline steps; dashed connectors (e–g) indicate that the corresponding post-mapping steps can be optional, otherwise the OUT2.sam file directly undergoes the assembly process (h). Please refer to Supplementary Information for a detailed description of MToolBox workflow steps