bio-population-genetics-rare-variant-association - Rare-variant gene and region association testing
Aggregates rare variants by gene or region to run burden, SKAT, SKAT-O, ACAT, or annotation-weighted STAAR tests with explicit masks.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Build variant masks
- Run burden tests
- Run SKAT tests
- Run SKAT-O tests
- Run ACAT tests
- Run STAAR tests
- Account for imbalance
- Validate burden files
Inputs
- Genotype data
- Phenotype data
- Covariate data
- Variant annotations
- Gene-set files
- Mask definitions
- Null-model predictors
- MAF cutoffs
- Annotation groups
Outputs
- Gene-level association results
- Region-level association results
- Set-test statistics
- Association p-values
- Variant masks
- Validation diagnostics
- Null-model predictors
Requirements
- regenie 3.4 or later
- SAIGE 1.3 or later
- SKAT R package 2.2 or later
- STAAR R package 0.9.7 or later
- Compatible R environment
- Installed command-line tools