Upload a VCF file to create a sample

You can upload a single VCF file and define it as a sample so that the variants that are listed in the file can be annotated with Ion Reporter™ Software. A sample can contain only one VCF file. It cannot contain multiple VCF files.

Ensure that the VCF file meets the following criteria so the file is successfully imported into Ion Reporter™ Software.

  • Annotate Variants analysis workflows accept VCF files that conform to the 4.1 VCF standard only.

  • Annotate Variants analysis workflows also accept a compressed VCF file that use BCF, VCF, GZ, and BCF.GZ file formats. Ion Reporter™ Software decompresses the GZ file and uses the resulting VCF or BCF file.

  • Use CHROM as a column heading name to designate chromosome position in the VCF file.

Note: If you plan to use an uploaded VCF and the GRCh38 reference with the Annotate Variants analysis workflow in Ion Reporter™ Software, ensure that you include the following text in the header line of the VCF file: ##reference=GRCh38.

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

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

  5. Click Close to exit the Upload VCF dialog box.
  6. In the Samples step, select the VCF file that you uploaded, then click Add to Sample.
  7. In Sample Name, enter a descriptive and unique sample name, then click Add to Sample List.

    Sample names are limited to 255 characters, and can be any combination of alphanumeric characters plus spaces, periods (.), hyphens (-), and underscores (_).

    Your VCF file now appears in the Files Included list and the number of data files is shown in the field with dotted lines.

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

    Option

    Description

    Set the value of an 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 column of the attribute heading.

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

    Add a new attribute.

    Use this option to add a new custom sample attribute. For more information, see Create a custom sample attribute.

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

The new sample is added to the Samples table.

The sample or samples are now ready for analysis with the Annotate Variants analysis workflow. For more information, see Launch an analysis.

Related Topics
Parent topic: Sample import options