IonReporterUploader command-line utility

You can use the IonReporterUploader command-line utility to transfer or upload sequencing run results files to Ion Reporter™ Software, then define samples that are based on the transferred files. The IonReporterUploader command-line utility uses your Ion Reporter™ Software account credentials to transfer run data from Torrent Suite™ Software to the organization on the specified Ion Reporter™ Server. The utility, which is available at, supports these types of file 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.

  • Uploads of samples from hg19 and GRCh38 reference genomes only. Although the E-coli and animal reference genomes can be used in Torrent Suite™ Software, these reference genomes are not supported in Ion Reporter™ Software.

  • To upload samples from other reference genomes, you can build a plugin that includes any reference genome. For more information, see Programming guidelines for Ion Reporter Software plugins.

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

The 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.

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