HAP-SAMPLE2

HAP-SAMPLE2 simulates genotype-phenotype data to facilitate power analyses and evaluate statistical learning methods in association studies, extending the original HAP-SAMPLE tool to handle population admixture and rare variant analysis.

Key Features:

• Population Admixture Simulation: Users can create admixed populations or preserve substructures while introducing novel variation through artificial recombination.
• Rare Variant Analysis: The tool supports burden testing for rare variants using fixed and Madsen-Browning weighting schemes.
• Parameterizable Disease Models: Users can define parameters such as disease prevalence and allele effect sizes for both common and rare variant simulations.
• Large-Scale Data Compatibility: HAP-SAMPLE2 provides an efficient means for simulating complex datasets suitable for large-scale projects like the 1000 Genomes Project.

Scientific Applications:

• Power Analysis: HAP-SAMPLE2 facilitates power analyses in genetic association studies.
• Statistical Method Evaluation: The tool enables evaluation of statistical learning methods in association studies.
• Admixed Population Genetics: HAP-SAMPLE2 supports simulation of genotype-phenotype data in the context of population admixture.
• Rare Variant Association Testing: The tool enables simulation and burden testing frameworks for rare variant analysis.

Methodology:

HAP-SAMPLE2 uses data-based resampling for association studies with admixture, employing artificial recombination to introduce novel variation.