Abdullah Asım Emül, Mehmet Arif Ergün, Rumeysa Aslıhan Ertürk, Ömer Çinal, Mehmet Baysan
{"title":"VCF observer:一款用户友好型软件工具,用于对 VCF 文件进行初步分析和比较。","authors":"Abdullah Asım Emül, Mehmet Arif Ergün, Rumeysa Aslıhan Ertürk, Ömer Çinal, Mehmet Baysan","doi":"10.1186/s12859-024-05860-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Advancements over the past decade in DNA sequencing technology and computing power have created the potential to revolutionize medicine. There has been a marked increase in genetic data available, allowing for the advancement of areas such as personalized medicine. A crucial type of data in this context is genetic variant data which is stored in variant call format (VCF) files. However, the rapid growth in genomics has presented challenges in analyzing and comparing VCF files.</p><p><strong>Results: </strong>In response to the limitations of existing tools, this paper introduces a novel web application that provides a user-friendly solution for VCF file analyses and comparisons. The software tool enables researchers and clinicians to perform high-level analysis with ease and enhances productivity. The application's interface allows users to conveniently upload, analyze, and visualize their VCF files using simple drag-and-drop and point-and-click operations. Essential visualizations such as Venn diagrams, clustergrams, and precision-recall plots are provided to users. A key feature of the application is its support for metadata-based file grouping, accomplished through flexible data matrix uploads, streamlining organization and analysis of user-defined categories. Additionally, the application facilitates standardized benchmarking of VCF files by integrating user-provided ground truth regions and variant lists.</p><p><strong>Conclusions: </strong>By providing a user-friendly interface and supporting essential visualizations, this software enhances the accessibility of VCF file analysis and assists researchers and clinicians in their scientific inquiries.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"25 1","pages":"290"},"PeriodicalIF":2.9000,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373448/pdf/","citationCount":"0","resultStr":"{\"title\":\"VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison.\",\"authors\":\"Abdullah Asım Emül, Mehmet Arif Ergün, Rumeysa Aslıhan Ertürk, Ömer Çinal, Mehmet Baysan\",\"doi\":\"10.1186/s12859-024-05860-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Advancements over the past decade in DNA sequencing technology and computing power have created the potential to revolutionize medicine. There has been a marked increase in genetic data available, allowing for the advancement of areas such as personalized medicine. A crucial type of data in this context is genetic variant data which is stored in variant call format (VCF) files. However, the rapid growth in genomics has presented challenges in analyzing and comparing VCF files.</p><p><strong>Results: </strong>In response to the limitations of existing tools, this paper introduces a novel web application that provides a user-friendly solution for VCF file analyses and comparisons. The software tool enables researchers and clinicians to perform high-level analysis with ease and enhances productivity. The application's interface allows users to conveniently upload, analyze, and visualize their VCF files using simple drag-and-drop and point-and-click operations. Essential visualizations such as Venn diagrams, clustergrams, and precision-recall plots are provided to users. A key feature of the application is its support for metadata-based file grouping, accomplished through flexible data matrix uploads, streamlining organization and analysis of user-defined categories. Additionally, the application facilitates standardized benchmarking of VCF files by integrating user-provided ground truth regions and variant lists.</p><p><strong>Conclusions: </strong>By providing a user-friendly interface and supporting essential visualizations, this software enhances the accessibility of VCF file analysis and assists researchers and clinicians in their scientific inquiries.</p>\",\"PeriodicalId\":8958,\"journal\":{\"name\":\"BMC Bioinformatics\",\"volume\":\"25 1\",\"pages\":\"290\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2024-09-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373448/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s12859-024-05860-0\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12859-024-05860-0","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison.
Background: Advancements over the past decade in DNA sequencing technology and computing power have created the potential to revolutionize medicine. There has been a marked increase in genetic data available, allowing for the advancement of areas such as personalized medicine. A crucial type of data in this context is genetic variant data which is stored in variant call format (VCF) files. However, the rapid growth in genomics has presented challenges in analyzing and comparing VCF files.
Results: In response to the limitations of existing tools, this paper introduces a novel web application that provides a user-friendly solution for VCF file analyses and comparisons. The software tool enables researchers and clinicians to perform high-level analysis with ease and enhances productivity. The application's interface allows users to conveniently upload, analyze, and visualize their VCF files using simple drag-and-drop and point-and-click operations. Essential visualizations such as Venn diagrams, clustergrams, and precision-recall plots are provided to users. A key feature of the application is its support for metadata-based file grouping, accomplished through flexible data matrix uploads, streamlining organization and analysis of user-defined categories. Additionally, the application facilitates standardized benchmarking of VCF files by integrating user-provided ground truth regions and variant lists.
Conclusions: By providing a user-friendly interface and supporting essential visualizations, this software enhances the accessibility of VCF file analysis and assists researchers and clinicians in their scientific inquiries.
期刊介绍:
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.