SIMULATE

SIMULATE generates simulated genotypes for family members on chromosome maps of linked markers that are unlinked to a specified affection-status locus for downstream linkage analysis.

Key Features:

• Chromosome-Based Simulation: Employs a chromosome-based approach using a crossover formation (CF) process to determine the number and locations of crossovers along entire chromosomes measured in Morgans.
• Multilocus Data Generation: Efficiently generates simulated multilocus data across any number of loci on a chromosome, exceeding capabilities of methods used in SLINK or SIMLINK.
• Incorporation of Genetic Interference: Directly incorporates genetic interference into crossover simulations.
• Marker Affection-Status Constraint: Simulates genotypes for maps of linked markers that are explicitly unlinked to a specified affection-status locus.
• Output Compatibility: Produces outputs compatible with the UNKNOWN, ISIM, LSIM, and MSIM components of the SLINK package.

Scientific Applications:

• Human Linkage Analysis: Provides simulated genotype data for evaluating linkage analysis methods and interpreting recombination patterns in human genetics.
• Pedigree Data Simulation: Generates pedigree-level multilocus datasets with realistic crossover events for studies of inheritance and disease-susceptibility loci.

Methodology:

SIMULATE models crossovers using a chromosome-based crossover formation (CF) process to set crossover number and positions in Morgans and outputs data formatted for analysis with the UNKNOWN, ISIM, LSIM, and MSIM components of the SLINK package.