In the world of genomics, data ownership and portability are fundamental principles that every researcher and clinician should embrace. With the increasing complexity of genomic datasets and the critical importance of long-term data accessibility, having the ability to export your data in multiple formats is not just convenient, it’s essential. This is where the gautil export commands shine, providing researchers with powerful tools to liberate their data from proprietary formats and ensure long-term accessibility.

Understanding Data Freedom

Data freedom in genomics means having unrestricted access to your own data, regardless of the software or platform used to generate it. This includes the ability to easily export annotation data from the new VSWarehouse 3 assessment catalog files (.catalog). These files are the optimized databases that allow for the complex assignment and interpretation workflows. It also includes the annotation files (.tsf) created when curating custom annotations with the Convert Wizard. When your data is trapped in proprietary formats, you risk losing years of careful curation and analysis if software becomes unavailable or workflows change. It also makes it difficult to share and collaborate.

The gautil command-line utility addresses this challenge head-on by providing multiple export pathways that preserve both the content and structure of your genomic data. Whether you’re working with variant catalogs, custom annotation tracks, or complex multi-sample datasets, the command-line gautil tool ensures that your data remains accessible and portable across different platforms and analysis environments. This tool is included by default with all VarSeq installations and allows for easy export from the optimized Golden Helix formats on Windows, Mac, and Linux.

Getting Started

The gautil tool can be found in the VarSeq install folder along side the VarSeq application. On Windows and Linux this is in the folder with the VarSeq executable. You can open this location from the VarSeq application by going to “Tools” > “Open Folder” > and selecting “VarSeq Install Folder”. On Mac following these same steps will open the VarSeq application bundle, and you can find the gautil executable in the “Tools” folder.

You can run the gautil command without any arguments to see the help message and get started with the available commands:

./gautil

The gautil Export Arsenal

writetxt: Universal Text Export

The writetxt command serves as the universal translator for your genomic data, converting complex catalog structures into clean, tab-delimited text files that can be read by virtually any analysis tool or programming language.

./gautil writetxt VariantCatalog.catalog test.txt

This command excels at exporting specific fields from your catalogs, allowing you to create custom datasets tailored to your analysis needs. The tab-delimited format ensures compatibility with R, Python, Excel, and countless other tools, making it the perfect choice when you need maximum flexibility in downstream analysis. The field selection capability means you can export only the annotation fields relevant to your current research question, streamlining your workflow and reducing file sizes.

writexlsx: Structured Excel Export

When you need to share data with collaborators or create publication-ready tables, the writexlsx command transforms your genomic data into professionally formatted Excel spreadsheets with intelligent field grouping and color-coded headers.

./gautil writexlsx VariantCatalog.catalog test.xlsx --group="Region,0,1,2"  --group="Details,3,4,5"

This command is particularly powerful for complex datasets where logical grouping enhances readability. The ability to create custom field groups means you can organize clinical annotations separately from functional predictions, making it easier for reviewers and collaborators to navigate your data.

writevcf: Standards-Compliant Variant Export

The writevcf command ensures that your variant data can be seamlessly integrated into any genomics pipeline by exporting it in the industry-standard VCF format.

./gautil writevcf VariantCatalog.catalog test.vcf --fields=0,1,2,3,4,5

This command is essential when you need to move variant data between different analysis platforms or share data with collaborators using different software ecosystems. The VCF format’s widespread adoption means your exported data will be compatible with virtually every genomics tool, from variant callers to annotation pipelines. The command automatically handles the complex formatting requirements of VCF files, including proper genomic ordering and metadata preservation.

Liberating Your Golden Helix Data

Golden Helix catalogs and custom annotations are the product of thoughtful analysis and careful curation. In order to be able to maximize the value of this data in the Golden Helix software suite and with collaborators we provide and support tools like gautil which allow for easy conversion between different data formats. The gautil export commands ensure that this valuable data remains accessible regardless of future software changes or platform migrations. Whether you’re working with variant catalogs containing thousands of curated variants or custom annotation tracks with specialized scoring systems, these commands provide multiple pathways to data freedom.

Conclusion

Data freedom is not just about having access to your data; it’s about ensuring that the valuable insights and annotations you’ve developed remain useful and accessible throughout the entire lifecycle of your research. The gautil export commands provide the tools necessary to achieve this freedom, offering multiple export pathways that preserve both the content and structure of your genomic data.

By utilizing these export capabilities, you’re not just protecting your current analysis, you’re investing in the long-term value of your research data. Whether you’re preparing for software migrations, sharing data with collaborators, or simply ensuring that your hard work remains accessible, the gautil export commands provide the foundation for sustainable genomics data management.

If you’re interested in implementing data freedom practices in your genomics workflows or need assistance with data export strategies, please don’t hesitate to contact our team at [email protected]. We’re here to help you get the most out of your genomic data, today and in the future.