Var2GO: a web-based tool for gene variants selection.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Variant calling generates large datasets, making gene filtering and annotation challenging.
• Existing tools can be time-consuming and may lead to loss of important information during gene filtering.
• Manual gene-by-gene investigation is often required, increasing complexity and potential for errors.

Purpose of the Study:

• To introduce Var2GO, a web-based tool for efficient annotation and filtering of variants and genes.
• To provide a user-friendly interface for biologists to manage and analyze high-throughput sequencing data.
• To streamline the process of identifying biologically relevant genes from variant calling results.

Main Methods:

• Var2GO accepts raw Variant Calling Format (VCF) files or annotated variant tables.
• It utilizes SnpEff for preliminary variant annotation and converts data into a database.
• Genes are automatically annotated with Gene Ontology (GO) terms, enabling keyword-based filtering.

Main Results:

• Var2GO successfully annotates genes with GO terms across three domains.
• The tool allows users to filter genes based on specific GO annotations and keywords.
• Demonstrated effectiveness using exome sequencing data, showcasing its practical application.

Conclusions:

• Var2GO offers a novel, topic-based approach for narrowing gene searches in variant calling analysis.
• It empowers non-bioinformaticians to handle complex variant data via an intuitive web interface.
• Provides a comprehensive pipeline from raw VCF files to extracting relevant biological insights.