. Author manuscript; available in PMC: 2022 Jan 13.

Published in final edited form as: Genet Med. 2021 Jul 13;23(10):1838–1846. doi: 10.1038/s41436-021-01230-w

Table 1. Modes for running Neptune.

Neptune can be run in multiple different modes, specified by command line parameters.

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	Pre-report file, project configuration	Populates the pre-report with the final set of data. Separate in case it needs to run in a PHI environment
reanalyze	VIP annotated vcf	Takes an existing VIP annotated vcf, shows differences to current VIP