Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants

Abstract

AbstractThe Variant Call Format (VCF) file is providing a structured and comprehensive text file that contains essential information about variant positions in the genome, as well as other critical details, such as alleles, genotype calls, and quality scores. Due to its rich data and format, the VCF file has become an increasingly popular resource for researchers and clinicians alike, enabling them to interpret and understand genomic variation data. However, analyzing and visualizing these files poses significant challenges, demanding access to diverse resources and a robust set of features for in-depth exploration. We introduce Variant Graph Craft (VGC), a VCF file visualization and analysis tool offering a wide range of features for exploring genetic variations, including extraction of variant data, intuitive visualization of variants, and the provision of a graphical representation of samples, complete with genotype information. Furthermore, VGC seamlessly integrates with external resources to offer valuable insights into gene function and variant frequencies in sample data. VGC offers gene function and pathway information from Molecular Signatures Database (MSigDB) for GO terms, as well as KEGG, Biocarta, Pathway Interaction Database, and Reactome. Additionally, the tool also provides a dynamic link to gnomAD for variant information, and includes ClinVar data for pathogenic variant information. VGC operates locally, assuring users of data security and privacy by eliminating the need for cloud-based VCF uploads. It supports the Human Genome Assembly Hg37, ensuring compatibility with a wide range of data sets. With its versatility, VGC accommodates various approaches exploring genetic variation data, and can be tailored to the specific needs of the user by using optional phenotype input data. In conclusion, VGC is a useful resource for exploring genetic variation in a secure and user-friendly environment. With its user-tailored set of features, this tool enables researchers and clinicians to easily explore and understand genomic variation data in a comprehensive and accessible manner. From identifying specific genetic mutations to analyzing patterns of variation across the genome, the VCF file visualization and analysis tool is an essential tool for those working in the field of genomics. VGC is freely available athttps://sites.brown.edu/gmilab/variantgraphcraft/