SEQMINER

SEQMINER annotates, queries, and integrates sequence variant files (VCF and BCF) and summary association statistics (METAL and RAREMETAL) to enable scalable analysis of genetic variants in sequence-based association studies of complex traits.

Key Features:

• Annotation and Querying: Annotates sequence variant files (VCF, BCF) and summary association statistics (METAL, RAREMETAL) for variant-level and summary-statistic queries.
• Integration of Bioinformatics Databases: Integrates various bioinformatics databases to enrich variant annotations and support downstream analyses.
• Linkage Disequilibrium (LD) Exploration: Investigates LD structure between variants to inform interpretation of association signals and genetic architecture.
• Statistical Method Support: Provides infrastructure for distributing and applying novel statistical methods in sequence-based association studies.
• Scalability for NGS Data: Implemented as an R package to address computational demands and support efficient handling of large-scale next-generation sequencing datasets.

Scientific Applications:

• Consortium-scale Association Studies: Enables analysis using public summary association statistics in multi-cohort and consortia studies of complex traits.
• Genetic Association Interpretation: Supports interpretation of genotype-phenotype associations to elucidate genetic architecture of complex diseases.
• Clinical Translation Support: Facilitates analyses (annotation and LD assessment) that can guide clinical interpretation and follow-up of variant associations.

Methodology:

Processes VCF/BCF files and METAL/RAREMETAL summary statistics using R for efficient data handling and analysis; methods were demonstrated using datasets from the 1000 Genomes Project.