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.