GVAF: generalized, flexible filtering software for annotated variant files.

Background: In the rapidly advancing field of genomics, many tools have been developed to interpret genetic variants using next-generation sequencing (NGS) data. However, these tools often produce annotated variant files in different formats, which require specific software or programming skills to filter and analyze.

Objective: To provide a filtering tool that can be used with diverse variant annotation tools without requiring specific software or programming skills.

Methods: We developed Germline Variant Annotation and Filtering (GVAF), a command-line software tool that can handle annotated variant files in any table-shaped format. GVAF offers powerful filtering operations without the need for additional software or programming expertise.

Results: Built on the Java framework and bash scripts, it provides extensive features, including flexible filtering rules, recognition of genotype-related fields from variant call format (VCF) files, and customizable result generation. GVAF also integrates easily into existing data analysis pipelines. Compared to other tools, GVAF offers a broader range of functionalities, making it more flexible and intuitive for managing annotated variant files.

Conclusion: This GVAF software and online manual is publicly available at https://www.sysbiolab.org/gvaf for academic users and is designed to streamline the variant interpretation process, aiding researchers in producing meaningful results.