UPDhmm

UPDhmm implements a hidden Markov model for detecting uniparental disomy through high throughput sequencing data from trio assays.

Key Features:

• Trio-based UPD detection: Analyzes genotypes in a trio to infer hidden states of normal, father isodisomy, mother isodisomy, father heterodisomy, and mother heterodisomy.
• HMM-based inference: Uses a hidden Markov model to identify both whole-chromosome and segmental uniparental disomy events.

Scientific Applications:

• UPD detection in clinical genomics: Identifies uniparental disomy, a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent rather than one copy from each parent.
• Trio sequencing analysis: Processes high throughput sequencing data from family trios to distinguish between normal inheritance and paternal or maternal isodisomy and heterodisomy.

Methodology:

The package employs a hidden Markov model that analyzes genotypes in trio assays to infer hidden states representing normal inheritance, father isodisomy, mother isodisomy, father heterodisomy, and mother heterodisomy.