LDSO

LDSO simulates whole diploid population genomic data using the gene-dropping method to model population histories and genetic forces for population genetics research.

Key Features:

• Simulation of genetic forces: Simulates mutation, random genetic drift, changes in population size, selection, and pedigree structure that influence linkage.
• Trait genetic architecture: Models additivity, dominance, and epistasis affecting trait architecture.
• Linkage disequilibrium and IBD outputs: Produces optional outputs for linkage disequilibrium statistics and identity by descent between chromosomal segments.
• Pedigree-based simulations: Simulates genomic data within known pedigrees to capture recent population history and long-range LD structure.
• Implementation: Implemented as a self-contained Fortran90 application.

Scientific Applications:

• Evaluation of statistical methods: Provides realistic simulation environments for developing and validating statistical methods in genomics.
• Optimization of experimental designs: Enables simulation of diverse scenarios relevant to mapping studies to inform experimental design decisions.
• Fine-mapping strategies: Facilitates optimization of fine-mapping strategies by simulating pedigree-aware long-range LD and inheritance patterns.

Methodology:

Uses the gene-dropping method (MacCluer et al., 1986) to model whole diploid population histories; implemented in Fortran90.