In the GUI, after you have run a computation, the Sample-Variant Table on the main Variants Tab gets updated with Variant frequencies, and you can export the data from that table to a file manually. The CLI allows you to trigger the generation of the report using the “report variantHits” command (see section 3.4.12.2 for the usage statement). You can then choose to process this report on your own to prioritize which Variants are the most promising for user verification in the GUI. The CLI also allows you to export the computed alignments, if you wish to analyze them by other means, using the “report alignment” command (see section 3.4.12.1 for the usage statement).