Upload a BAM file to create a sample or samples

You can manually upload one or more BAM files into Ion Reporter™ Software.

BAM files are available as output files from Torrent Suite™ Software. These BAM files contain sample reads that can be mapped to the reference genome, or unmapped. If the output file is mapped, the software makes both BAM and BAI files available as output files in Torrent Suite™ Software. If the file is unmapped, only the BAM file is available. If you upload BAM files that are unmapped into Ion Reporter™ Software, the software adds the mapping. Also, if files require additional reference mapping, those reference sequences are added. You can use these BAM output files to manually upload files to Ion Reporter™ Software.

Note: You can set the Tmap Mapped Files Enable Re-map parameter to True if you want mapped BAM files that you upload to be remapped. For more information, see Customize tuning parameters.

The name of a BAM file that is uploaded to Ion Reporter™ Software cannot exceed 200 characters.

  1. In the Samples tab, click Overview.
  2. Click Define Samples > Manual.
  3. In the Samples step, click Upload BAM.
  4. In the Upload BAM Sample File dialog box, click Select file to navigate to the file that you want to upload, then click Upload BAM.

    The BAM file is added to the list of files in the Samples step.

  5. Click Close to close the dialog box.
  6. In the Samples step, select one or more BAM files, then click Add to Sample.
  7. In Sample Name, enter a descriptive and unique name, then click Add to Sample List.

    Sample names can be any combination of alphanumeric characters plus spaces, periods (.), dashes (-), and underscores (_). There is a 255-character limit.

  8. Click Next.
  9. (Optional) In the Attributes step, set the value for a new or 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, then 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.

  10. Click Next.
  11. In the Review step, click Save.

The new sample or samples are added to the Samples table.

The sample or samples are now ready for analysis. For more information, see Launch an analysis.