Ped-sim

Ped-sim simulates pedigree structures and identical-by-descent (IBD) segments using sex-specific genetic maps and crossover interference models to study how recombination patterns affect IBD distribution among relatives.

Key Features:

• Sex-Specific Genetic Maps: Supports sex-specific and sex-averaged genetic maps to model male/female recombination rate differences that influence the number and distribution of IBD segments.
• Crossover Interference Modeling: Simulates crossover events using a crossover interference model or a Poisson model for inter-crossover distances to represent interference effects on crossover spacing and IBD variance.
• Parental Sex Assignment: Allows random assignment or user-specified parental sexes when using sex-specific maps to control parental sex configurations in simulations.
• Output Files: Produces [out_prefix].seg containing IBD segments, [out_prefix].fam as a PLINK family file listing simulated relatives, and [out_prefix].log with simulation details.
• Simulation Comparisons: Simulates combinations of map types and interference models to evaluate their impact on IBD segment distribution and pairwise IBD variance.

Scientific Applications:

• Modeling IBD Sharing: Studies IBD sharing among close relatives where accurate modeling of shared segments is critical.
• Recombination Effects on IBD: Evaluates how sex-specific recombination rates and crossover interference affect the number and distribution of shared IBD segments and the standard deviation of pairwise IBD proportions.
• Genetic Linkage and Disease Studies: Supports investigations of genetic linkage, hereditary disease mapping, and relatedness inference in population genetics.
• Simulation Validation: Enables comparison of simulated IBD rates to real data by combining sex-specific maps with interference modeling.

Methodology:

Simulations use sex-specific or sex-averaged genetic maps, model crossover events with either a crossover interference model or a Poisson model for inter-crossover distances, allow random or specified parental sex assignment, and run combinations of these settings to evaluate impacts on IBD segment distribution.