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

Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli
2014 Computer applications in the biosciences : CABIOS  
Motivation: The increasing availability of mitochondria-targeted and off-targeted sequencing data in Whole Exome and 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
more » ... 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 (VCF) 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: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/. Contacts:
doi:10.1093/bioinformatics/btu483 pmid:25028726 pmcid:PMC4201154 fatcat:zaukpoou6rekpd3yjrlmmhvfm4