Create a Sequence Variant Baseline workflow preset

You can create a custom Sequence Variant Baseline workflow preset in Ion Reporter™ Software to detect somatic variants. You can later add the custom baseline to an analysis workflow that you can use as a baseline control for analyses.

If you import the custom sequence variant baseline, the target regions file that was used to create the baseline must be available in the software to ensure that the imported baseline appears in the list of available sequence variant baselines. When you add the baseline to an analysis workflow, the same target regions files that is used to create the baseline must also be used in the analysis workflow.

IMPORTANT! A sequence variant baseline can be used with Ion AmpliSeq™ somatic samples only. Do not use a custom baseline for the detection of germline variants, as a germline variant can occasionally be misclassified as a sequencing error.

The sequencing run or runs that are used to create the sample data must use the same Ion Torrent chip type and same Ion AmpliSeq™ panel. For example, if an SVB will be applied to a sequencing run that used a 540 chip and custom Ion AmpliSeq™ panel, then the germline samples used to create the SVB must have been sequenced with the 540 chip and same custom Ion AmpliSeq™ panel.

  1. In the Workflows tab, click Presets, then click Create Preset > Sequence Variant Baseline.
  2. In the Baseline Type step of the Create Sequence Variant Baseline workflow bar, select the baseline type that corresponds to the type of libraries that you use.

    Baseline type

    Description

    AmpliSeq Somatic

    Ion AmpliSeq™

  3. Select a reference genome.
    • GRCH38

    • hg19

  4. Select the Target Regions file that corresponds to the panel. If the target regions file is not available in the panel, you can upload the file.
  5. Click Next.
  6. In the Parameters step, do not change parameters from the default settings unless you understand how the change can affect your analysis. Click Next.
  7. In the Samples step, do the following:
    1. Select the samples to be used in the baseline creation.

      All samples must be normal (non-tumor). It is recommended that at least 20 samples be used to create the custom sequence variant baseline. The use of multiple samples increases the robustness of the sequence variant baseline.

      If you do not see your samples in the table, see Sample definition for information on how to upload or define a sample.

    2. Select the Chip Type that was used for the sample data.

      All samples that you select for the sequence variant baseline must use the same chip type.

  8. Click Next.
  9. In the Confirm step, enter a name, or accept the default name, then enter an optional description for the baseline.
  10. Click Launch.

The baseline creation job is started and the baseline with its status now appears on the screen. When the job completes, the baseline is added to the Workflow Presets screen and is available to add to an analysis workflow. For more information, see Apply a baseline workflow preset to an analysis workflow.