Define samples with a CSV file

When the uploaded data files in BAM or VCF formats are available in Ion Reporter™ Software, you can then use a CSV file to define the data as samples in Ion Reporter™ Software software. The CSV file defines sample names and attributes for an associated BAM or VCF file.

If there are editable sample attributes that you want to redefine, you can update the attributes in the CSV file, then upload the file into Ion Reporter™ Software as a new sample. You can then the new sample to launch a new analysis. For more information on which sample attributes can be edited, see Sample attributes.

You can also edit an existing CSV file to add attributes to existing samples. For example, you can add attributes to the samples that were not included in the Torrent Suite™ Software Planned Run, or add new attributes that are required to reuse the samples in a different analysis.

You can download an example sample definition CSV file from the Define Samples screen. Add the file location for the related sample BAM file and customize the example sample definitions CSV file to create a CSV file for upload. For more information, see Create a sample CSV file to define samples.

  1. In the Samples tab, in the Overview screen, click Define Samples > Import from CSV.
  2. Click Select File, then browse to the CSV file.
  3. Ensure that the displayed filename is correct, then click Upload.

    The software checks that the sample is valid.

  4. In the Samples step, click Next.
  5. In the sample list, ensure that the sample information is correct.
  6. (Optional) In the Attributes step, set the value for a new or pre-existing attribute:

    Option

    Description

    Set the value of a pre-existing attribute.

    1. Click the field in the column of the attribute heading.

    2. Enter a value or select a value from a list.

    Add an attribute and set its value.

    1. Click Add Attribute and select an attribute from the list.

    2. Click the field in the column of the attribute heading.

    3. Enter a value or select a value from a list.

    Add a new attribute.

    For more information, see Create a custom sample attribute.

  7. Click Next.
  8. In the Review step, click Save.

The Samples tab opens, with the new sample listed in the Samples table.

The new samples are ready for analysis. For more information, see Launch an analysis.