haplocheck

haplocheck detects contamination in mitochondrial and whole-genome sequencing studies by leveraging phylogeny-based analysis to distinguish genuine heteroplasmy from contamination.

Key Features:

• Phylogeny-based analysis: Uses mitochondrial phylogenetic information to distinguish genuine heteroplasmic sites from contamination.
• mtDNA-only operation: Operates solely on mitochondrial DNA (mtDNA) data without requiring nuclear genome analysis.
• WGS applicability: Can be applied to whole-genome sequencing (WGS) datasets to detect mitochondrial contamination within broader sequencing studies.
• Computational efficiency: Avoids the computational expense associated with nuclear genome-based contamination methods by relying on mtDNA phylogeny.
• Mitochondrial copy number assessment: Quantifies the influence of mitochondrial copy number variation on contamination detection outcomes.

Scientific Applications:

• Validation of contamination estimates: Demonstrated high concordance between mitochondrial and nuclear DNA contamination estimates using data from the 1000 Genomes Project.
• Assessment of mtDNA copy number effects: Evaluates how variations in mitochondrial copy numbers affect the detection and estimation of contamination.

Methodology:

Performs phylogeny-based analysis of mitochondrial DNA to differentiate genuine heteroplasmy from contamination.