VarAFT

VarAFT annotates and prioritizes genomic variants in VCF files to identify candidate disease-causing mutations by integrating multiple annotation sources, applying configurable filtration parameters across samples, and performing BAM-based coverage and quality checks.

Key Features:

• Annotation and Prioritization: Annotates VCF variants using dbNSFP, OMIM, HPO, Gene Ontology, pathway annotations, UMD-Predictor, and Human Splicing Finder to support variant prioritization.
• Multi-Sample Integration: Combines data from multiple samples across individuals to support analyses of Mendelian inheritance patterns, cancer genomics, and population genetics.
• Optimized Filtration Parameters: Applies configurable filtration and prioritization parameters with the ability to store and reapply optimized parameter sets across large datasets.
• Coverage Analysis and Quality Check: Performs coverage analysis and quality checks using BAM files to evaluate data integrity for variant calls.

Scientific Applications:

• Mendelian disease gene identification: Prioritizes candidate pathogenic variants for Mendelian inheritance analyses.
• Cancer genomics: Supports somatic and germline variant filtering and prioritization in cancer studies.
• Population genetics: Enables variant filtering and aggregation across cohorts for population-level analyses.
• Clinical diagnostics using NGS: Assists in identifying clinically relevant variants from next-generation sequencing data for diagnostic interpretation.

Methodology:

Annotation of VCF files using dbNSFP, OMIM, HPO, Gene Ontology, pathway annotations, UMD-Predictor, and Human Splicing Finder; integration of multiple samples across individuals; configurable filtration and prioritization with storable/reapplicable parameter sets; and coverage analysis and quality checks from BAM files.