Sample import options

Sample data are imported into Ion Reporter™ Software in four ways.

• Sample data are typically transferred from Torrent Suite™ Software when the sequencing run is complete. Sample data can be transferred automatically based on the IonReporterUploader plugin settings that are in the Torrent Suite™ Software Planned Run. For more information, see Automatic transfers of sequencing run data.

• Data from instrument sequencing runs can be transferred manually. You can also upload sample data directly from a BAM or VCF data file. Sample files in VCF format are typically uploaded to annotate the variants in the file, with an Annotate Variants analysis workflow. After you upload the sample files, you must complete the steps to define the sample before it is analyzed in Ion Reporter™ Software. For more information, see Upload a BAM file to create a sample or samples and Upload a VCF file to create a sample.

• You can also import sample data directly into Ion Reporter™ Software if you use one of the following:

  • A CSV file. For more information, see Define samples with a CSV file.

  • An Ion PGM™ Dx System. For more information, see Import samples from Torrent Suite Dx Software.

  • The IonReporterUploader command-line utility. For more information, see IonReporterUploader command-line utility.

  • An external data file. For more information or assistance with this option, contact your Field Bioinformatics Specialist (FBS).