Pedcheck

Pedcheck identifies Mendelian genotype incompatibilities in pedigree data to detect erroneous genotypes that could compromise linkage analysis.

Key Features:

• Error-checking algorithms: Implements four distinct error-checking algorithms to detect different types of pedigree errors.
• Parent-offspring compatibility checks: Includes parent-offspring compatibility testing to flag direct Mendelian violations.
• Single-locus likelihood-based statistics: Uses single-locus likelihood-based statistics to identify and rank individuals most likely to contain errors.
• Scalability: Performs rapid processing of large datasets for efficient error screening.
• Input formats: Supports multiple input formats for pedigree and genotype data.
• Diagnostic output: Produces detailed diagnostic information to guide correction of identified inconsistencies.
• Algorithmic foundation: Employs algorithms derived from VITESSE.

Scientific Applications:

• Linkage analysis quality control: Detects and removes Mendelian inconsistencies prior to linkage analysis to prevent spurious results.
• Mendelian inconsistency detection: Identifies erroneous genotypes and ranks likely error carriers within pedigrees.
• Large-pedigree curation: Facilitates error detection and correction in extensive pedigrees where manual checking is impractical.

Methodology:

Applies a suite of four error-checking algorithms, including parent-offspring compatibility tests and single-locus likelihood-based statistics, to input pedigree/genotype data and outputs detailed diagnostics.