SimPed

SimPed generates simulated haplotype and genotype data for pedigrees across dense marker maps to support simulation-based genetic analyses.

Key Features:

• Scalability: Handles pedigrees of virtually any size and complexity.
• High marker density: Generates data across more than 20,000 marker loci, including dense SNP marker maps.
• Marker allelic types: Supports generation of both diallelic and multiallelic loci.
• Customizable genetic parameters: Permits specification of genetic map distances and haplotype or allele frequencies.
• Linkage disequilibrium modeling: Produces data in linkage equilibrium or disequilibrium, accommodating strong intermarker LD.
• Simulation engine: Employs Monte Carlo methods to generate haplotype and genotype datasets.

Scientific Applications:

• Linkage analysis: Provides simulated data for parametric and nonparametric linkage analyses, including analyses on dense SNP maps.
• Family-based association studies: Supports simulation of familial genotype data for family-based association testing.
• Method evaluation: Enables evaluation of methods that estimate haplotype frequencies in pedigree data.
• Error estimation: Allows assessment of type I error rates arising from intermarker linkage disequilibrium.
• Empirical p-value estimation: Facilitates estimation of empirical p values for linkage and family-based association studies.

Methodology:

SimPed uses Monte Carlo methods to simulate haplotype and genotype data that reflect specified genetic map distances, haplotype or allele frequencies, and linkage equilibrium or disequilibrium states.