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XVCF: Exquisite visualization of VCF data from genomic experiments
Ghaida Almuneef1, Abdulrhman Aljouie2, Yahya Bokhari3
1Artificial Intelligence and Bioinformatics Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
SLAS Technology
|June 20, 2026
Summary
XVCF is a new R Shiny App that simplifies the visualization and summarization of genomic variation data. This user-friendly tool addresses challenges in interpreting large datasets, making genomic analysis more accessible.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- High-throughput sequencing generates large genomic datasets, posing visualization and interpretation challenges.
- Existing tools for visualizing genetic variants from VCF files often require command-line expertise, limiting accessibility.
- There is a need for user-friendly, graphical tools to summarize and visualize genomic variation data.
Purpose of the Study:
- To develop an interactive, GUI-based tool for summarizing and visualizing genomic variation data.
- To provide an accessible solution for researchers facing challenges in interpreting large-scale genomic datasets.
- To facilitate the analysis of both germline and cancer genomic data.
Main Methods:
- Developed XVCF, an interactive Shiny App using the R programming language.
- Utilized R packages 'vcfR' and 'maftools' for data visualization and quality control.
- Implemented a graphical user interface (GUI) for interactive data loading, summarization, and visualization.
Main Results:
- XVCF provides an easy-to-use interface for interactive genomic data summarization and visualization.
- The tool extracts key information like read depth, mapping quality, genotype, and allele frequency.
- XVCF analyzes cancer genomic data using 'maftools' to generate oncoplots, lollipop plots, and gene summaries.
- XVCF is freely available on GitHub and compatible across different operating systems.
Conclusions:
- XVCF offers a user-friendly solution for visualizing and summarizing genomic variation data.
- The tool simplifies complex genomic data analysis through its intuitive GUI and powerful R Shiny framework.
- XVCF enhances accessibility to genomic data interpretation for researchers lacking extensive programming knowledge.
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