Create a copy number baseline for low-coverage whole-genome libraries

Users with the analyze role can create a copy number baseline for use with whole genome libraries with whole genome amplification and low coverage, such as Aneuploidy. This type of copy number baseline is for use with Ion ReproSeq™ PGS Kits.

IMPORTANT! Use the default parameter settings unless you are an advanced user. Contact a Field Bioinformatics Specialist (FBS) for help.

In the Workflows tab, click Presets, then click Create PresetCopy Number Baseline.
The Create Copy Number Baseline screen opens.
Make the following selections in the Create Copy Number Baseline screen.
1. Select Low-coverage Whole-Genome.
2. Select a reference genome.
  - GRCH38
  - hg19
Click Next.
In the CNV Detection Type step, under Germline (CNV Informatics Baseline), click Configure parameters.
In the Configure Parameters screen, accept the default settings or adjust the appropriate parameters, then click Done.
Click Next.
In the Samples step, select the required number of samples for the baseline. For accurate baselines, ensure that the samples selected for the baseline have been run with the same panel as the baseline.

If you do not select the minimum number of samples that are required for the baseline, you cannot proceed.

Note: Only samples designated in the software as male are available to be selected to be used to create the CNV Informatics Baseline.
Click Next to advance to the Confirm step.
In the Confirm step, enter a name for the baseline, or use the default name, and enter an optional description for the baseline.
Click Create Baseline.

The baseline creation job is started and its status is shown in the Presets screen.

When the baseline creation is complete, it is locked and shown in the Presets screen with a State of Successful and is available for use in the software. The new baseline can only be added to analysis workflows that are used for whole genome libraries with whole genome amplification and low coverage.

If the State of a copy number baseline is Failed, place the pointer over the row of the copy number baseline and click View Log to open the log in a separate browser tab, or click Download Log to download the log file. This record can help you troubleshoot the failure.