IonReporterUploader command-line utility

The IonReporterUploader command-line utility is an command-line alternative to the IonReporterUploader plugin that is included with Torrent Suite™ Software. You can download the IonReporterUploader command-line utility at: http://iru.ionreporter.thermofisher.com/.

You can use the IonReporterUploader command-line utility to transfer analysis results files to Ion Reporter™ Software and to set up samples, based on the transferred files. The IonReporterUploader command-line utility uses the login ID to transfer run data from Torrent Suite™ Software to Ion Reporter™ Software. The utility supports the following types of transfers.

Transfers of a single BAM or VCF file.

The name of a BAM file that is uploaded to Ion Reporter™ Software cannot exceed 200 characters.
Transfers of all results files for a Torrent Suite™ Software analysis.
Transfers of results files that are in a single flat folder.
Transfers of multiple files that are not restricted to a single folder.

You can later analyze the samples with Ion Reporter™ Software. The IonReporterUploader command-line utility can be run on the Torrent Server, or can be run on any standard (and current) computer that runs Linux™, macOS™, or Windows™ Operating System. You can enter IonReporterUploader command-line utility options through command line arguments, or through a properties file.

Note: IonReporterUploader command-line utility should not be used for uploading samples from references other than hg19 and GRCh38. Although E-coli and animal reference genomes can be used in Torrent Suite™ Software, they are not supported in Ion Reporter™ Software.

IonReporterUploader command-line utility supports the upload of combined run results that are output by using the Combine Alignments option in the Torrent Suite™ Software. Uploads of combined run results are not supported when the IonReporterUploader plugin is used in Torrent Suite™ Software.

Java™ 11 is required to run IonReporterUploader command-line utility without errors.

Note: Java™ is included with Ion Reporter™ Software. If you are running Java™ 9 or later, you need to also have Java™ 8 for the JNLP to act correctly to visualize variants from Ion Reporter™ Software with the Broad Institute Integrative Genomics Viewer (IGV).

For more information about IonReporterUploader command-line utility, see the IonReporterUploader Command-Line Utility User Guide (Pub. No. MAN0017648).