Define samples with one or more BAM files

Sequence results from multiple libraries prepared from the same sample or multiple sequencing results from the same library can be combined for increased analytical power. You can also use a single BAM file to define the sample.

Note: Analyses might fail if the BAM files have different values for the SM (Sample Name) key in the RG (Read Group) (@RG) tag when you create single fusion sample from multiple BAM files. The multiple BAM files that are used to define a sample in Ion Reporter™ Software must each have the same Sample Name as is defined in the Read Group tag.

  1. In the Samples tab, in the Overview screen, click Define Samples > Manual.

    The name of your organization is shown on the left of the screen, and sample files for your organization are listed in the table.

  2. (Optional) Click Upload BAM, click Select File, then navigate to and select the desired BAM file, then click Open.
  3. Click VCF above the table to filter for VCF files.

    Files that are transferred by the IonReporterUploader plugin in Torrent Suite™ Software appear under data/IRU_Uploads, in time-stamped folders. Demonstration data files appear under the demodata folder.

  4. To view the files in either the upload directory or the demodata directory, expand the menu on the left that matches the organization name, then expand the data file directory that contains data files of interest.
  5. Use these steps to select the data files that will be used as samples in the software.
    1. Select one or more BAM files from the list of available files, then click Add to Sample.
    2. Enter a Sample Name, then click Add to Sample List.
    3. (Optional) Repeat steps a and b to define additional samples.
  6. Click Next.
  7. In the Attributes step, you can set sample attribute values or add a new attribute and set its value.

    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.

    You can create custom sample attributes that can be used for future analyses. For more information, see Create a custom sample attribute.

  8. Review the samples listed under Samples ready to import!

    • If the sample name and the data files are correct, click Save.

    • To change the sample, click Previous.

  9. If the sample information is correct, click Next.

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

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

Related Topics
Parent topic: Define a sample manually