RAREsim

RAREsim performs haplotype simulations of rare variant genetic data that emulates real data.

Key Features:

• MAC Bin-Based Pruning: Uses the expected number of variants in MAC bins, either from default parameters or estimated from target data, to guide variant pruning.
• Probabilistic Variant Pruning: Probabilistically prunes variants from an abundance of rare variants simulated by HAPGEN2.
• Realistic Haplotype Generation: Produces haplotypes that emulate real sequencing data with respect to total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Scientific Applications:

• Rare Variant Simulation: Generates simulated haplotypes for rare variant genetic studies that match properties of real sequencing data.
• Genetic Data Emulation: Creates reference datasets with realistic allele frequency spectra and haplotype structure for method development and validation.

Methodology:

RAREsim takes an abundance of rare variants simulated by HAPGEN2 and probabilistically prunes variants using the expected number of variants in MAC bins.