# Where to find Microarray sample quality metrics in DRAGEN Array Cytogenetics and Emedgene

### **DRAGEN Array Cytogenetics Analysis**

**cyto call** command generates **gt\_sample\_summary** file (CSV or JSON) which provides the following metrics:

Autosomal Call Rate

Call Rate

Log R Ratio Std Dev

Sex Estimate

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-e24b1fc3dde86c2cda01cb1824457b083a9afb37%2Fimage1.jpg?alt=media)

**cyto annotate** command generates **cyto annotation** file (JSON) per sample to report sample-level, chromosome-level, and event-level metrics and annotations. See DRAGEN Array User Guide [Cytogenetics Annotation JSON file](https://help.dragenarray.illumina.com/product-guides/output-files#cytogenetics-annotation-json-file) for more details on the reported metrics.

### **Emedgene**

#### **Lab Tab**

Under "SAMPLE QUALITY" section the following metrics are available:

Family Member

Quality

Sex Validation

Autosomal Call Rate

Call Rate

Log R Dev

For additional details regarding these metrics, see Emedgene User Guide: [Lab tab](https://help.emg.illumina.com/emedgene-analyze-manual/reviewing_a_case/lab_tab) and [Sample quality section](https://help.emg.illumina.com/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section).

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-954fd98e393100b63f9e085c0cbef1952f9c83eb%2Fimage2.jpg?alt=media)

Under the Sample ID name, click **Dragen report** link to open **Cytogenetics Array Report**. This page contains sample and chromosomal information derived from the DRAGEN Array **cyto annotation** JSON file.

**Sample Quality**

Sample Sex

% LoH

Median CN

Call Rate

Log R Dev

**Chromosome Quality**

% Het

LRR Median

LRR Dev

% LoH

Median CN

Mean CN

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-6aee7178c1945fe3054fb0eb17872df52dfd76b3%2Fimage3.jpg?alt=media)

#### **Analysis Tools tab**

Click on a variant from the list and the Variant page window pops up. Select Quality on the left menu. Under "Quality" section the following metrics are available:

VCF Filter

Likelihood Ratio

Mean LRR

Copy Number

Mosaic Fraction

CNV Quality

Size

Bin Count

For additional details regarding these metrics, see Emedgene User Guide [Variant page](https://help.emg.illumina.com/emedgene-analyze-manual/variant_page/variant_page) and [Quality tab](https://help.emg.illumina.com/emedgene-analyze-manual/variant_page/quality_section).

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-873a25002ee21755de56afefcd612fdc26fa1a97%2Fimage4.jpg?alt=media)

For more information, see [DRAGEN Array User Guide](https://help.dragenarray.illumina.com/) and [Emedgene User Guide](https://help.emg.illumina.com/).

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