CLI Reference¶
Overview of VNtyper 2 command-line interface.
Usage: vntyper [global-options] <command> [command-options]
Global options must be placed before the subcommand.
Global Options¶
| Option | Type | Default | Description |
|---|---|---|---|
-v, --version | flag | N/A | Show version and exit |
-l, --log-level | choice | INFO | Logging level: DEBUG, INFO, WARNING, ERROR, CRITICAL |
-f, --log-file | path | stdout | Log output file path. For pipeline and cohort commands, automatically set to <output-dir>/pipeline.log or <output-dir>/cohort.log when --output-dir is provided |
--config-path | path | bundled config | Path to a custom config.json. If omitted, default bundled configuration is used |
Commands¶
| Command | Description |
|---|---|
pipeline | Run the full genotyping pipeline |
install-references | Download and set up reference files |
report | Generate HTML summary report |
cohort | Aggregate multi-sample results |
online | Submit analysis to vntyper.org |
calibrate | Generate and evaluate explicit opt-in dominance profiles |