Table 1 Modes for running Neptune.
From: Neptune: an environment for the delivery of genomic medicine
Command | Input(s) | Description |
|---|---|---|
annotate | vcf, project configuration | Annotates vcf with data from the VIP. Marks if a variant has been previously seen or needs review. |
renderPreReport | VIP annotated vcf, configuration information for external data, report template, project configuration | Loads data from external sources, creates a structured output files. |
renderFinalReport | Prereport file, project configuration | Populates the prereport with the final set of data. Separate in case it needs to run in a protected health information (PHI) environment. |
reanalyze | VIP annotated vcf | Takes an existing VIP annotated vcf, shows differences to current VIP. |
