MitoAnalyzer

mitoAnalyzer is a software package that provides a general approach for the analysis of mitochondrial DNA (mtDNA) in next-generation sequencing studies, using whole-genome sequencing data. It has two components:

  • mitoCaller -- an algorithm designed specifically to identify mtDNA variants (i.e., homoplasmies and heteroplasmies)
  • mitoCaller incorporates sequencing error rates at each base in a likelihood calculation and allows allele fractions at a variant site to differ among individuals. It relies on a genotype likelihood calculation, described below:
  • Genotype Likelihood Calculation:
    Genotype Likelihood Calculation
  • mitoCalc and fastMitoCalc -- programs to estimate mtDNA copy number in a cell directly from sequencing data
  • mitoCalc and fastMitoCalc estimate mtDNA copy number based on the observed ratios of sequence coverages between mtDNA and autosomal DNA.
  • The most recent update, fastMitoCalc is a program that can estimate mtDNA copy number highly accurately but is more than 100 times faster than mitoCalc.
  • fastMitoCalc can rapidly analyze hundreds of thousands of genomes, thereby facilitating association studies of mtDNA copy number with quantitative traits or nuclear variants.

Intramural Research Program Bioinformatics Informatics