VAPr

VAPr performs variant analysis and prioritization by integrating annotation data with scalable, reproducible storage and filtering to support interpretation of population-scale whole-exome and whole-genome sequencing cohorts.

Key Features:

• Annotation integration: Integrates outputs from ANNOVAR and MyVariant.info to consolidate variant annotations.
• Flexible storage and filtering: Uses MongoDB for storage and provides flexible querying and filtering of cohort-scale variant datasets.
• Scalability and reproducibility: Implements scalable, reproducible workflows for analysis of large-scale genomic data, including population-scale WES and WGS.

Scientific Applications:

• Population-scale genomic studies: Analysis and prioritization of variants in population-scale whole-exome and whole-genome sequencing cohorts.
• Disease association studies: Prioritization of candidate variants for downstream association analyses in cohort datasets.
• Evolutionary biology: Identification and comparison of variants relevant to evolutionary and population-genetic analyses.
• Personalized medicine: Prioritization of clinically relevant variants for precision-medicine research.

Methodology:

Implements a Python package that integrates ANNOVAR and MyVariant.info annotations with MongoDB-based storage and flexible filtering to provide scalable, reproducible workflows for cohort WES/WGS variant analysis.