SVAFotate

SVAFotate annotates structural variants (SVs) with allele frequency and related metrics from multiple population-scale datasets to enable estimation of population allele frequencies for SVs and support variant stratification.

Key Features:

• Annotation with Allele Frequencies: Integrates allele frequencies and associated metrics from existing SV datasets to annotate individual SV calls.
• VCF File Enhancement: Enriches VCF (Variant Call Format) files with metrics that assist in distinguishing common versus rare structural variants.
• Facilitation of Rare Disease Analysis: Provides allele frequency annotations used for filtering and prioritizing SVs in rare disease studies.

Scientific Applications:

• Filtering and Prioritization: Supports filtering strategies to isolate significant SVs from large datasets by annotating them with population allele frequencies.
• Classification by Frequency: Enables classification of SVs as common or rare to aid studies of genetic variation and rare disease genetics.

Methodology:

Matches structural variant calls across multiple datasets to compile comprehensive allele frequency information and embeds these annotations into VCF records.