ArticleBMC bioinformatics2022
Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 25 citations in OpenAlex.
- Unified long-read panel for Parkinson's and repeat expansion disorders.NPJ Parkinson's disease · 2026Article
- Intragenic deletions from whole genome sequencing of 1054 suicide deaths.Research square · 2026Article
- Diagnostic utility of clinical genome reanalysis in rare pediatric disorders using long-read sequencing.HGG advances · 2026Article
- needLR: long-read structural variant annotation with population-scale frequency estimation.Bioinformatics (Oxford, England) · 2026Article
- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
- BICEP: an extension to indels and copy number variants for rare variant prioritisation in pedigree analysis.bioRxiv : the preprint server for biology · 2026Article
- Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.GigaScience · 2026Article
- The biomedical landscape of genomic structural variation in the qatari population.Nature communications · 2026Article
- The Impact of Structural Variation on Alzheimer's Disease in the Alzheimer's Disease Sequencing Project.Research square · 2026Article
- GeNePi: a graphics processing unit enhanced next-generation bioinformatics pipeline for whole-genome sequencing analysis.Briefings in bioinformatics · 2026Article
- needLR: Long-read structural variant annotation with population-scale frequency estimation.ArXiv · 2025Article
- Compound Heterozygous Structural Variants in Cases with Unsolved PRKN-Associated Parkinson's Disease.Movement disorders : official journal of the Movement Disorder Society · 2025Article
- Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report.Cureus · 2025Article
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- Review
- Comprehensive genome analysis and variant detection at scale using DRAGEN.Nature biotechnology · 2025Article
- Identification of 2 novel noncoding variants in patients with Diamond-Blackfan anemia syndrome by whole genome sequencing.Blood advances · 2025Article
- Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.Genome research · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundIdentification of deleterious genetic variants using DNA sequencing data relies on increasingly detailed filtering strategies to isolate the small subset of variants that are more likely to underlie a disease phenotype. Datasets reflecting population allele frequencies of different types of variants serve as powerful filtering tools, especially in the context of rare disease analysis. While such population-scale allele frequency datasets now exist for structural variants (SVs), it remains a challenge to match SV calls between multiple datasets, thereby complicating estimates of a putative SV's population allele frequency.
resultsWe introduce SVAFotate, a software tool that enables the annotation of SVs with variant allele frequency and related information from existing SV datasets. As a result, VCF files annotated by SVAFotate offer a variety of metrics to aid in the stratification of SVs as common or rare in the broader human population.
conclusionsHere we demonstrate the use of SVAFotate in the classification of SVs with regards to their population frequency and illustrate how SVAFotate's annotations can be used to filter and prioritize SVs. Lastly, we detail how best to utilize these SV annotations in the analysis of genetic variation in studies of rare disease.
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