> 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/data-sources/gerp.md).

# GERP

### Overview

GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint (Rejected Substitutions). DRAGEN Annotation uses GERP++ which is based on a significantly faster and more statistically robust maximum likelihood estimation procedure to compute expected rates of evolution.

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

Davydov, Eugene V., et al. "Identifying a high fraction of the human genome to be under selective constraint using GERP++." *PLoS computational biology* **6.12** e1001025 (2010). <https://doi.org/10.1371/journal.pcbi.1001025>
{% endhint %}

### Source Files

#### Example GRCh37

GRCh37 file is a TSV format

```tsv
chr     position    GERP
1       12177       0.83
1       12178       -0.206
1       12179       -0.492
1       12180       -1.66
1       12181       0.83
1       12182       0.83
1       12183       -0.417
1       12184       0.83
```

#### Example GRCh38

GRCh38 file is a lift-over BED format

```tsv
chr     pos_start   pos_end     GERP
1       12646       12647       0.298
1       12647       12648       2.63
1       12648       12649       1.87
1       12649       12650       0.252
1       12650       12651       -2.06
1       12651       12652       2.61
1       12652       12653       3.97
```

#### Parsing

From the CSV file, we are interested in columns:

* `chr`
* `position`
* `GERP`

### Known Issues

None

### Download URL

#### GRCh37

<http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html>

#### GRCh38

The data is not available for GRCh38 on GERP++ website, and was obtained from <https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/>

### JSON Output

```json
"gerpScore": 1.27
```

| Field     | Type  | Notes           |
| --------- | ----- | --------------- |
| gerpScore | float | Range: -∞ to +∞ |


---

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