VarioWatch

VarioWatch annotates and analyzes human genomic variants from next-generation sequencing data to provide comprehensive functional annotations and risk-level evaluations.

Key Features:

• High-Speed Annotation: Annotates millions of genomic variants in minutes or seconds for large-scale datasets.
• Comprehensive Variant Annotation: Provides annotations for known SNPs and novel variants using NCBI, UniProt, KEGG, and GO and supports NCBI build 36.3 and NCBI build 37.2.
• Functional Analysis: Assesses effects on splice sites and insertions/deletions (in/dels).
• Risk Level Decision Tree: Applies a decision tree to evaluate and assign risk levels to analyzed variants.
• Variant Filtering and Visualization: Filters variant subsets by criteria such as risk level or genomic region and visualizes up to 1000 target variants.
• Batch Processing and Gene-Level Annotation: Processes batches of markers and retrieves gene ontology, function, pathway, disease associations, and related PubMed articles.

Scientific Applications:

• Gene Association Studies: Identifies and analyzes statistically significant genomic markers including SNPs and short tandem repeat polymorphisms in human studies.
• Next-Generation Sequencing Variant Annotation: Rapidly annotates large datasets generated by next-generation sequencing technologies.
• Functional Impact Assessment and Primer Design: Supports SNP functional impact analysis and provides information useful for primer design in target gene re-sequencing.

Methodology:

Annotates variants using public databases NCBI, UniProt, KEGG, and GO with support for NCBI builds 36.3 and 37.2; performs functional analysis of splice sites and in/dels; applies a decision tree for risk evaluation; supports batch processing, filtering, and visualization of variants.