> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/annotation/v3.27/data-sources/dann.md).

# DANN

### Overview

DANN uses the same feature set and training data as CADD (Combined Annotation-Dependent Depletion) to train a deep neural network (DNN). CADD is an algorithm designed to annotate both coding and non-coding variants, and has been shown to outperform other annotation algorithms. DANN improves on CADD (which uses Support Vector Machines (SVMs)) by capturing non-linear relationships by using a deep neural network instead of SVMs. DANN achieves about a 19% relative reduction in the error rate and about a 14% relative increase in the area under the curve (AUC) metric over CADD’s SVM methodology.

{% hint style="info" %}
**Publication**

Quang, Daniel, Yifei Chen, and Xiaohui Xie. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. *Bioinformatics* **31.5** 761-763 (2015). <https://doi.org/10.1093/bioinformatics/btu703>
{% endhint %}

### TSV File

#### Example

```tsv
chr     grch37_pos  ref     alt     DANN
1       10001       T       A       0.16461391399220135
1       10001       T       C       0.4396994049749739
1       10001       T       G       0.38108629377072734
1       10002       A       C       0.36182020272810128
1       10002       A       G       0.44413258111779291
1       10002       A       T       0.16812846819989813
```

#### Parsing

From the CSV file, we are interested in all columns:

* `chr`
* `grch37_pos`
* `ref`
* `alt`
* `DANN`

### GRCh38 liftover

The data is not available for GRCh38 on DANN website. We performed a liftover from GRCh37 to GRCh38 using crossmap.

### Known Issues

None

### Download URL

<https://cbcl.ics.uci.edu/public_data/DANN/>

### JSON Output

```json
"dannScore": 0.27
```

| Field     | Type  | Notes          |
| --------- | ----- | -------------- |
| dannScore | float | Range: 0 - 1.0 |


---

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