SNPsim

SNPsim simulates haplotypes and single nucleotide polymorphisms (SNPs) using a modified coalescent model with recombination to generate realistic haplotype blocks for population genetics and genetic association study simulations.

Key Features:

• Modified coalescent model with recombination: Implements a modified coalescent model with recombination for simulating genealogies.
• Non-homogeneous recombination rates: Allows specification of non-homogeneous recombination rates across genomic regions to reproduce haplotype blocks observed in the human genome.
• Multiple mutation models: Supports multiple mutation models.
• Flexible demographic histories: Accommodates flexible demographic histories to simulate varied evolutionary scenarios.
• Genotype and haplotype output: Generates haplotype samples and diploid biallelic genotypes.

Scientific Applications:

• Human genomic architecture: Simulates haplotype block structure to study linkage disequilibrium and genomic architecture in the human genome.
• Genetic association studies: Produces realistic SNP and haplotype datasets for evaluating association study designs and methods for identifying disease-related genes.
• Population genetics and evolution: Models evolutionary scenarios and demographic histories for population genetics analyses.

Methodology:

Uses a modified coalescent model with recombination, incorporates non-homogeneous recombination rates, supports multiple mutation models and flexible demographic histories, and outputs haplotypes and diploid biallelic genotypes.