> 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/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-germline-enrichment.md).

# DRAGEN Germline Enrichment

<figure><img src="/files/ic6iIIH9tw2WuU6Ma42I" alt=""><figcaption></figcaption></figure>

Select the DRAGEN\_Germline\_Enrichment\_4-5-4 Pipeline. This pipeline can traditionally only be run with the low coverage settings, due to the post-collapsed coverage rates required.

**WARNING**: Deviation from these instructions (including adding additional options) may cause pipeline failure.

### Coverage Rate Minimums

The following coverage rates are the minimums recommended for each of the various workflows:

* Coverage Rate >20x for Germline Methyl-Only
* Coverage Rate >30x for Germline Methyl + VC

1. Select the necessary input files for the run, including sample inputs (.fastq, .fastq.ora, .bam, or .cram files), and a Target BED File.
2. Select a reference genome. 5-base is compatible with any methyl\_cg references. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.
3. To Enable Methylation Aware Algorithms, select "True" for Enable 5-Base Methylation-Aware Algorithms.<br>

   <figure><img src="/files/zU9A6pfSzXLBv5TPyqBd" alt=""><figcaption></figcaption></figure>
4. For Report Methylation at Variant Positions, select "default".<br>

   <figure><img src="/files/ODlTYIrh9pMAn9hsY2uX" alt=""><figcaption></figcaption></figure>
5. In the Variant Calling Options section:
   1. Set Emit Ref Confidence to GVCF
   2. Set Enable VCF File Output to true
   3. Set Enable CNV calling to false
   4. Set CNV Enable In-Run Panel of Normals to false
   5. Set CNV GC Bias Correction to false
   6. Set Enable SV calling to false<br>

      <figure><img src="/files/XJTUG7AOQu9J3xsncUwj" alt="" width="563"><figcaption></figcaption></figure>
6. Start the analysis


---

# 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/dragen-5-base/run-analysis-setup/ica-analysis-setup/dragen-germline-enrichment.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.