mixoviz

mixoviz detects and quantifies diploid-triploid mixoploidy from whole genome sequencing (WGS) data by analyzing variant allele signals to estimate proportions of diploid and triploid cells.

Key Features:

• Detection methodology: Analyzes variant calls with atypical B-allele frequencies and leverages trio-based sequencing data (child, mother, father) to isolate mixoploidy signals.
• Quantitative analysis: Estimates the ratio of diploid to triploid cells by solving linear equations derived from allele-depth and genotype information.
• Input requirements: Operates on tabix-indexed VCF files containing trio calls with allele depths (AD tag) and genotype quality (GQ tag), compatible with outputs such as GATK3.

Scientific Applications:

• Clinical diagnosis of chromosomal mosaicism: Identifies and quantifies diploid-triploid mixoploidy in patient WGS data to support diagnosis of mosaic conditions and rare disease investigations.
• Comparison with cytogenetics: Enables assessment of WGS-derived mixoploidy estimates against cytogenetic test results.

Methodology:

Computational steps include identifying variant calls with atypical B-allele frequencies, isolating trio-based signals using child–mother–father genotype and allele-depth information, and solving linear equations to estimate diploid versus triploid cell proportions.