ArticleNucleic acids research2017
VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations.The plant genome · 2026Article
- Machine learning method for the prediction of Bedaquiline-resistantLife science alliance · 2026Article
- igv-reports: embedding interactive genomic visualizations in HTML reports to aid variant review.Bioinformatics (Oxford, England) · 2026Article
- A bacterial toxin-antitoxin system involved in an unusual response to genotoxic stress.EMBO reports · 2025Article
- GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants.BMC bioinformatics · 2025Article
- Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants.BMC bioinformatics · 2024Article
- TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome.Nature communications · 2024Article
- 123VCF: an intuitive and efficient tool for filtering VCF files.BMC bioinformatics · 2024Article
- Identifying genes associated with genetic control of color polymorphism in the pearl oysterEvolutionary applications · 2023Article
- Phenotype-aware prioritisation of rare Mendelian disease variants.Trends in genetics : TIG · 2022Review
- A review of deep learning applications in human genomics using next-generation sequencing data.Human genomics · 2022Review
- PhenGenVar: A User-Friendly Genetic Variant Detection and Visualization Tool for Precision Medicine.Journal of personalized medicine · 2022Article
- Computational approaches for predicting variant impact: An overview from resources, principles to applications.Frontiers in genetics · 2022Review
- Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity.Science immunology · 2021Article
- SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.Communications biology · 2021Article
- Set-theory based benchmarking of three different variant callers for targeted sequencing.BMC bioinformatics · 2021Article
- re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files.PeerJ · 2021Article
- The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity.Science immunology · 2020Article
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- CD70 Deficiency Associated With Chronic Epstein-Barr Virus Infection, Recurrent Airway Infections and Severe Gingivitis in a 24-Year-Old Woman.Frontiers in immunology · 2020Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.