User Manual¶

Welcome to the VariantValidator User Manual.

This manual describes how to use the VariantValidator software suite. It is intended for researchers, bioinformaticians, clinical scientists and software developers who wish to validate, normalise, map and format genetic sequence variant descriptions using the VariantValidator software suite.

The documentation is organised into task-focused sections, allowing users to quickly find information relevant to their workflow.

Getting Started¶

If you have not yet installed VariantValidator, begin with the Installation Guide.

Choose an Interface¶

VariantValidator can be accessed through several interfaces, allowing you to choose the workflow that best suits your requirements.

Local Installation¶

A local installation provides access to the complete VariantValidator software suite, including:

VariantValidator
VariantFormatter
gene2transcripts
hgvs2reference
Python API
Command-line interface (CLI)

Installation instructions are provided in the Installation Guide.

Web Interface¶

The VariantValidator web interface provides interactive validation and formatting of sequence variant descriptions directly from your web browser.

Access the web interface at:

https://variantvalidator.org/

Documentation for the web interface will be added in a future release.

REST API¶

The VariantValidator REST API provides programmatic access to the VariantValidator software suite over HTTP and is intended for software integration, automated workflows and high-throughput pipelines.

Access the REST API at:

https://rest.variantvalidator.org/

Documentation for the REST API will be added in a future release.

Using VariantValidator¶

VariantValidator validates, normalises and maps genetic sequence variant descriptions.

Topics include:

Using VariantFormatter¶

VariantFormatter formats and converts genetic sequence variant descriptions between supported representations.

Topics include:

Additional Tools¶

VariantValidator includes several utility tools that support common workflows.

gene2transcripts¶

The gene2transcripts tool retrieves transcript information for genes.

Topics include:

hgvs2reference¶

The hgvs2reference tool retrieves reference sequences corresponding to supported HGVS sequence variant descriptions.

Topics include:

Reference Documentation¶

The reference documentation contains information shared across the VariantValidator software suite.

Topics include:

Need Help?¶

If you encounter problems:

Verify that VariantValidator has been installed and configured correctly by following the Installation Guide.
Review the documentation for the relevant tool.
Search the project's GitHub Issues for known problems.
Open a GitHub Issue to report a bug or request a feature.
Contact the VariantValidator support team via the support page.

Documentation Structure¶

Section	Description
Installation Guide	Installing, configuring and verifying VariantValidator.
Web Interface	Interactive validation and formatting using the hosted VariantValidator website. Documentation coming soon.
REST API	Programmatic access to VariantValidator over HTTP. Documentation coming soon.
VariantValidator CLI	Validate, normalise and map sequence variant descriptions from the command line.
VariantValidator Python API	Validate, normalise and map sequence variant descriptions from Python.
VariantFormatter CLI	Format and convert supported sequence variant descriptions from the command line.
VariantFormatter Python API	Format and convert supported sequence variant descriptions from Python.
gene2transcripts CLI	Retrieve transcript information for genes from the command line.
gene2transcripts Python API	Retrieve transcript information for genes from Python.
hgvs2reference Python API	Retrieve reference sequences from supported HGVS sequence variant descriptions.
Supported Input Formats	Supported HGVS and non-HGVS input formats accepted throughout the software suite.
Output Formats	Output formats returned by the VariantValidator software suite.
Transcript Selection	Transcript selection strategies and transcript models.
Errors and Error Codes	Reference guide to VariantValidator errors, warnings and diagnostic messages.

As the VariantValidator software suite continues to evolve, this documentation will be updated to reflect new features, interfaces and best practices. The aim is to provide clear, practical guidance for both new and experienced users while supporting reproducible and reliable variant analysis workflows.