Augment an existing VCIB baseline workflow preset

You can augment an existing Variability Correction Information Baseline (VCIB) workflow preset with additional samples.

When baseline is augmented, new samples are run, the size of each systematic affect encoded in the baseline is estimated, and a correction is applied to remove the effect. These added samples need not be normal and should be diverse so as to capture likely systematic variation.

  1. In the Workflows tab, click the Presets screen, then click Create Preset > Copy Number Baseline.
  2. Select a Baseline Type, then select your Target Regions file, then click Next.
  3. In the Algorithm step, select the Start with an existing CNV Baseline checkbox, then select a baseline from the list.

    The list of baselines will be limited to baselines that were created with the Target Regions BED file that was selected in the Baseline Type step.

  4. In the Samples step, select samples to use in the baseline.

    By default, the software prompts you to add another 48 samples. However, you can set the number to 1 or more.

    To distinguish between non-normal and normal samples, you can use the Normal designation in the analysis workflow. This designation has no effect on the analysis. Only the original Normal samples in the first baseline creation are treated as Normal samples in the augmented baseline.

  5. Click Configure Parameters.
  6. In the Configure Parameters dialog box, click Cnv Baseline Creation, then Advanced. Set the Minimum number of samples required to add to an existing baseline parameter to reflect the number of samples that you add.
  7. Click Done, then click Next.
  8. In the Samples step, select any additional samples to include in the CNV baseline workflow preset, then click Next.
  9. Enter a name for your baseline, or accept the default name, then enter an optional description, then click Create Baseline to save the updated workflow preset.

You can now add the augumented baseline to an analysis workflow. For more information, see Create an analysis workflow that contains a copy number baseline.