Import a custom annotation source

You can use your own annotation source files in Ion Reporter™ Software. If you have annotation data that you want to use, you must first create a new annotation set for the custom annotation source. Then, you can import the files into the new annotation set.

IMPORTANT! Annotation files that have been edited and uploaded from a computer running Microsoft™ Windows OS to an Ion Reporter™ Server running a Linux OS, might have additional characters added at the end of new lines. Use the dos2unix command to avoid potential errors with the software service caused by the characters.

There are four types of annotation sources that you can import into Ion Reporter™ Software. The types of annotation sources and the file formats required for each annotation source are as follows:

Note: Only one version of an annotation source can be used in an annotation set.

Annotation source type


File format for import

Genomic region

A set of regions


Gene set

A set of genes


Preferred transcript set

A set of transcripts



A set of variants


  1. In the Workflows tab, click Presets.
  2. Click Create Preset > Annotation Set.
  3. Enter a descriptive Name for the custom annotation set.
  4. (Optional) Enter a description for the custom annotation set.
  5. Select a custom annotation type from the drop-down list:
    • Genomic Region (Custom)

    • Gene Set (Custom)

    • Preferred transcript set (Custom)

    • VariantDB (Custom)

  6. Click the Create New tab.
  7. Enter a descriptive Name and Version for the custom annotation source.

    IMPORTANT! You can use the words AND, NOT or, OR in an annotation source name in Ion Reporter™ Software 5.12. Do not include these operators in an annotation source name if you use Ion Reporter Software 5.10 or earlier.

    IMPORTANT! When naming custom annotation sources and annotation versions:

    • Do not use capitalized AND, NOT, or OR. You can use lower case and, not, or or.

    • You cannot use two consecutive underscores (__).

    You cannot save the object using these characters.

  8. (Optional) Enter a description for the custom annotation source.
  9. Click Select File, then browse to and select your custom annotation source file, then click Open.
  10. Click Save.
  11. The new custom annotation source is added to the custom annotation set.