STAAR workflow

STAAR workflow implements the variant-Set Test for Association using Annotation infoRmation (STAAR) to perform rare variant association testing in whole genome sequencing studies, identifying associations with continuous and dichotomous traits while integrating functional annotations.

Key Features:

• STAAR and complementary tests: Implements the variant-Set Test for Association using Annotation infoRmation (STAAR) and supports SKAT, Burden, and ACAT tests.
• Integration of functional annotations: Incorporates qualitative functional categories and quantitative complementary functional annotations to increase power for rare variant analysis.
• Gene-centric and region-based analyses: Supports both gene-centric and broader genetic region approaches for genome-wide, candidate, and conditional analyses.
• Scalability and population structure handling: Designed for large whole genome sequencing datasets and accounts for population structure and relatedness.
• Workflow implementation and cloud optimization: Implemented in Workflow Description Language (WDL) and optimized for cloud-based platforms such as BioData Catalyst Powered by Terra.

Scientific Applications:

• Rare variant association studies: Detects associations between rare genetic variants and phenotypes in whole genome sequencing data.
• Genome-wide, candidate, and conditional analyses: Enables testing across genome-wide regions, targeted candidate regions, and conditional models.
• Continuous and dichotomous trait analysis: Applicable to both quantitative (continuous) and case-control (dichotomous) traits.
• Analysis in structured and related cohorts: Supports studies that require accounting for population structure and relatedness in large cohorts.

Methodology:

Implements the STAAR procedure (variant-Set Test for Association using Annotation infoRmation) and supports SKAT, Burden, and ACAT tests; integrates qualitative and quantitative functional annotations; supports gene-centric and genetic region approaches; implemented in WDL and optimized for BioData Catalyst Powered by Terra while accounting for population structure and relatedness.