VAS

VAS annotates millions of genetic variants by integrating variant lists with whole-genome genomic features to enable functional interpretation of coding and non-coding variation.

Key Features:

• Data Compression: Employs advanced data compression to transfer millions of variants from a client machine to the server in less than 50 megabytes of data.
• Comprehensive Data Integration: Integrates whole-genome transcription factor binding sites, open chromatin regions, and transcription data from the ENCODE consortium to link variants to genomic features.
• Customized Linking Algorithms: Uses server-side customized algorithms to efficiently link millions of variants with numerous whole-genome datasets.
• Efficiency in Annotation: Annotates both coding and non-coding variants at large scale and has annotated 6.4 million SNPs from the CEU trio without requiring pre-computations.
• Complementary Functionality: Complements tools focused on specific aims such as disease-risk assessment by providing broad, high-throughput annotation across diverse genomic features.

Scientific Applications:

• Large-scale variant annotation: Provides rapid first-pass identification of potentially interesting genetic variants from large variant lists for downstream analyses.
• Migraine meta-analysis: Applied to annotate variants identified in a migraine meta-analysis study.
• Personal Genomes Project datasets: Used to annotate multiple datasets from the Personal Genomes Project.

Methodology:

Combines advanced client-to-server data compression with server-side algorithms that link variant positions to extensive whole-genome datasets and supports annotation of large SNP sets without pre-computations.