# DRAGEN Array Cytogenetics Analysis

### DRAGEN Array - Cytogenetics Analysis

#### Cytogenetics Threshold Adjustment

When using **DRAGEN Array – Cytogenetics analysis** or **DRAGEN Array - Cytogenetics analysis + Emedgene interpretation** cloud analysis types, additional customization options will appear after product files are selected within Configuration Settings. Adjustments to these thresholds will be saved as part of the Configuration Setting. Thresholds can be adjusted based on results objectives. Adjusting thresholds will impact the number of events called and thus, the output in the VCF and JSON files.

The recommended thresholds/settings are pre-set within the software for any new configurations:

| Threshold                 | New Config | Min Value | Max Value |
| ------------------------- | ---------- | --------- | --------- |
| GTC Output                | False      | N/A       | N/A       |
| SNV VCF Output            | False      | N/A       | N/A       |
| CNV minimum size (kb)     | 0          | 0         | 250000    |
| CNV minimum probes        | 10         | 0         | 250000    |
| LOH minimum size (kb)     | 3000       | 0         | 250000    |
| LOH minimum probes        | 500        | 0         | 250000    |
| CNV Smoothing window size | 5          | 0         | 1000      |

### DRAGEN Array - Cytogenetics analysis + Emedgene interpretation

This analysis type integrates with [Emedgene](https://help.connected.illumina.com/emedgene) to display results in a user-friendly interface.

**Note:** Only specific versions of Emedgene and DRAGEN Array are compatible with each other. For more details see the [compatibility table](https://help.emg.illumina.com/emedgene-analyze-manual/supported-vcfs-variant-callers#compatibility-with-dragen-and-dragen-array-variant-callers) on the Emedgene help site.

#### Prerequisites

* You'll need an additional Emedgene subscription to be either "Array", "Professional", or "Enterprise" tier. You can also follow the [Illumina Software Registration Guide](https://help.connected.illumina.com/account-management/rg-registration) to obtain that subscription.
* To ensure proper integration with Emedgene (EMG), [ICA notifications](https://help.ica.illumina.com/project/p-notifications) must be enabled for the specific ICA BSSH-managed project. EMG relies on these notifications to detect when an analysis has successfully completed. To configure SNS ([Amazon Web Services Simple Notification Service](https://aws.amazon.com/sns/)) events in your managed ICA BSSH-managed project, follow these steps:
  * In the [ICA portal](https://ica.illumina.com/ica/), in the ICA BSSH-managed project (e.g. "BSSH Your Workgroup Name") navigate to the **Notifications** section via the left-hand menu.
  * Click **+ Create**, then select **ICA Event**.
  * Fill in the required fields as follows:
    * **Event:** Analysis Success
    * **Type:** SNS
    * **Address:** Provide the correct address based on your region (contact <techsupport@illumina.com> if unsure).
    * **Payload Version:** v4
    * **AWS Region:** This will be auto-populated based on the provided address.
    * (Recommended) Click **Send Test Message** to verify the configuration.
    * Click **Save** to complete the setup.

For more details on the prerequisites for this analysis, see the [Automatic Case Creation from ICA](https://help.emg.illumina.com/emedgene-analyze-manual/integrations/automatic-case-creation-from-ica-cyto-array-analysis) section in the Emedgene User Guide.\
For more details on limitations for this analysis see the [release notes](https://github.com/illumina-swi/dragen-array-docs/blob/DAv1.3/docs/product-guides/reference/release-notes/dragen-array-v1.2.0-release-notes/dragen-array-v1.2.0-cyto-emg-release-notes.md)

#### Applicable Arrays

For specific product compatibility, see the [Product & Analysis Compatibility](https://help.connected.illumina.com/dragen-array/overview/our-features#_product_compatability) table.