Define a single VCF file as a sample

You can define a new sample manually from an imported data file that uses VCF format.

You can use only one VCF file for this procedure, and you cannot combine multiple VCF files into a single sample. To combine samples from multiple files into a single sample, see Define samples with one or more BAM files.

  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 VCF, click Select File, then browse to, then select the desired VCF 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. Select the checkbox for the data file that contains the sample that you want to use, then click Add to Sample.

    When a data file directory is selected, the contents of the file list changes to reflect the files from the directory that you select. The Files included area lists the files for the sample, and the count of data files is displayed.

  6. At the top of the sample list, enter a descriptive name for the new sample. When the sample pane contains the correct data file and sample name for the sample, click Add to Sample List.

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

  7. Click Next.
  8. 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.

  9. 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.

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