FAVOR Essential Database: Whole-Genome Variant Annotation Scores for GRCh38/hg38

FAVOR Essential Database provides hundreds of functional annotation scores for all possible single-nucleotide variants and observed indels in the GRCh38/hg38 human genome build. The database, created by Hufeng Zhou, includes scores for conservation, epigenetics, protein function, and pathogenicity. These scores can be integrated with genotype data via the FAVORannotator tool to create annotated files for downstream analysis.

Use Cases

• Prioritizing pathogenic genetic variants based on integrated scores like CADD and MetaSVM.
• Analyzing variant impact on regulatory elements using epigenetic and transcription factor binding scores.
• Filtering variants for association studies using conservation and local nucleotide diversity metrics.
• Annotating custom variant lists with functional categories from Gencode and GeneHancer.

Strengths

• Covers 8,812,917,339 possible single-nucleotide variants and 79,997,898 observed indels.
• Provides hundreds of integrated functional annotation scores from multiple biological aspects.
• Designed for integration with the FAVORannotator tool to create all-in-one annotated files.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.
• Row count for the aggregated dataset is unknown, which may limit suitability assessment.

Provenance

Source

Harvard University Press

Collection Method

Compilation of annotation scores from various sources for the GRCh38/hg38 genome build.

Time Range

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Freshness

Last updated: unknown

Geography

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