> 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/v4.0/data-sources/revel.md).

# REVEL

### Overview

REVEL is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons.

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

Ioannidis, N. M. et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. *The American Journal of Human Genetics* **99**, 877-885 (2016). <https://doi.org/10.1016/j.ajhg.2016.08.016>
{% endhint %}

### CSV File

#### Example

```scss
chr,hg19_pos,grch38_pos,ref,alt,aaref,aaalt,REVEL
1,35142,35142,G,A,T,M,0.027
1,35142,35142,G,C,T,R,0.035
1,35142,35142,G,T,T,K,0.043
1,35143,35143,T,A,T,S,0.018
1,35143,35143,T,C,T,A,0.034
```

#### Parsing

From the CSV file, we're mainly interested in the following columns:

* `chr`
* `hg19_pos`
* `grch38_pos`
* `ref`
* `alt`
* `REVEL`

### Known Issues

{% hint style="warning" %}
**Sorting**

Since the input file contains positions for both GRCh37 and GRCh38, we split it into two **TSV** files (for the sake of better readability) with identical format. The positions for GRCh37 were sorted but not for GRCh38. So we re-sort the variants by position in the GRCh38 file.
{% endhint %}

{% hint style="warning" %}
**Conflicting Scores**

When there are multiple scores available for the same variant (i.e. the same position with the same alternative allele), we pick the highest score.
{% endhint %}

### Download URL

<https://sites.google.com/site/revelgenomics/downloads>

### JSON Output

```json
"revel":{ 
   "score":0.027
}
```

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


---

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