LOVD HGVS Syntax Checker Command-Line Interface¶

The LOVD HGVS Syntax Checker CLI provides access to the LOVD HGVS Syntax Checker from the command line using the VariantValidator Python package.

The CLI performs syntax checking of HGVS sequence variant descriptions and gene symbols using the locally installed LOVD HGVS Syntax Checker. If the local installation is unavailable, the CLI automatically falls back to the LOVD web API where supported.

Unlike the VariantValidator validation engine, the LOVD HGVS Syntax Checker does not require the VariantValidator databases or configuration to be installed.

The official LOVD HGVS Syntax Checker project is maintained by the LOVD team:

GitHub: https://github.com/LOVDnl/HGVS-syntax-checker
Documentation: https://lovd.nl/HGVS/

Installation¶

The LOVD HGVS Syntax Checker is distributed as part of the VariantValidator Python package.

Create and activate the recommended conda environment before installing VariantValidator.

conda env create -f environment.yml
conda activate vvenv

Install VariantValidator into the environment.

pip install .

The LOVD HGVS Syntax Checker itself must then be downloaded and configured locally.

python -m VariantValidator.bin.setup_lovd_syntax_checker

This command:

downloads the latest LOVD HGVS Syntax Checker release;
downloads the required support files;
builds the local syntax checker cache; and
prepares the command-line interface for use.

The LOVD project is actively developed. Running this command periodically is recommended to ensure that the latest version of the syntax checker and supporting reference data are installed.

Note

The LOVD HGVS Syntax Checker does not require the VariantValidator databases or configuration file.

If you wish to use the full VariantValidator validation engine, including transcript mapping and variant validation, see the Installation Guide.

Running the LOVD HGVS Syntax Checker¶

The command-line tool is:

lovd-hgvs-syntax-checker

Results are written as formatted JSON.

Checking an HGVS variant description¶

Submit a single HGVS sequence variant description using the --query option.

lovd-hgvs-syntax-checker \
    --query "NM_000059.4:c.7790G>A"

or

lovd-hgvs-syntax-checker \
    -q "NM_000059.4:c.7790G>A"

Checking a genomic variant¶

Genomic HGVS descriptions are handled in the same way.

lovd-hgvs-syntax-checker \
    -q "NC_000013.11:g.32355250G>A"

Checking a gene symbol¶

Gene symbols are checked using the --gene option.

lovd-hgvs-syntax-checker \
    -q BRCA2 \
    --gene

Writing results to a file¶

JSON output may be written directly to a file.

lovd-hgvs-syntax-checker \
    -q "NM_000059.4:c.7790G>A" \
    --output result.json

Output¶

The LOVD HGVS Syntax Checker always returns formatted JSON.

The returned information originates from the LOVD HGVS Syntax Checker and includes syntax validation results together with metadata describing the version of the checker used to perform the analysis.

Relationship to VariantValidator¶

The LOVD HGVS Syntax Checker performs syntax checking only.

If you require:

HGVS validation;
transcript mapping;
genomic projection;
protein consequence prediction;
transcript selection; or
variant formatting,

use the VariantValidator command-line interface instead.

See:

VariantValidator CLI