ArticleGenes2021
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Genomic Diversity of Human Respiratory Syncytial Virus (HRSV) Type A in a Pediatric Cohort in the United States After the Onset of the COVID-19 Pandemic.Microorganisms · 2026Article
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- Intrahost population dynamics of chikungunya virus in humans and naturally infectedVirus evolution · 2026Article
- Dengue virus genetic diversity in unvaccinated and vaccinated dengue-infected individuals: an observational analysis of the Butantan-DV phase 3 trial in Brazil.Lancet regional health. Americas · 2026Article
- Pathogenicity and transmissibility of bovine-derived HPAI H5N1 B3.13 virus in pigs.Emerging microbes & infections · 2025Article
- Vector surveillance during a major chikungunya outbreak in northwestern São Paulo state, Brazil.Npj viruses · 2025Article
- Clinical and laboratory profiles of Oropouche virus disease from the 2024 outbreak in Manaus, Brazilian Amazon.PLoS neglected tropical diseases · 2025Article
- Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance.Molecular biology and evolution · 2025Article
- Pathogenicity and transmissibility of bovine-derived HPAI H5N1 B3.13 virus in pigs.bioRxiv : the preprint server for biology · 2025Article
- Amplicon sequencing of pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle.PloS one · 2025Article
- Identification, functional analysis, and clinical applications of defective viral genomes.Frontiers in microbiology · 2025Review
- Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut.Virus evolution · 2025Article
- Entomological surveillance during a major CHIKV outbreak in northwestern São Paulo: insights from São José do Rio Preto.medRxiv : the preprint server for health sciences · 2024Article
- Article
- Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage.Viruses · 2024Article
- Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants.NPJ vaccines · 2024Article
- Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies.Virology journal · 2024Article
- Human adenovirus outbreak at a university campus monitored by wastewater and clinical surveillance.medRxiv : the preprint server for health sciences · 2024Article
- Development and application of a whole genome amplicon sequencing method for infectious salmon anemia virus (ISAV).Frontiers in microbiology · 2024Article
- Coding-complete genome of human alphaherpesvirus 1 isolated from a case of fulminant hepatitis.Microbiology resource announcements · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly customizable tool with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts variant call format (VCF) files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated with variants as historically tracked attributes, i.e., modifications can be recorded whenever an updated value is imported, thus keeping track of all changes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search function can be exploited to periodically check if pathogenicity-related data of a variant has changed over time. Patient recontacting ensuing from variant reinterpretation is made easier by iVar through the effective identification of all patients present in the database carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22,569 unique variants. iVar has proven to be a useful tool with good performance in terms of collecting and managing data from a medium-throughput laboratory.
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