> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/annotation/v3.27/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 |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://help.connected.illumina.com/annotation/v3.27/data-sources/revel.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.