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

# DRAGEN Germline Enrichment

Select the DRAGEN Germline Enrichment 4.6.2 Pipeline. This pipeline can traditionally only be run with the low coverage settings, due to the post-collapsed coverage rates required.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-69e4ba953dfdeedf8adedb81b26335139945e8aa%2Fimage%20(144).png?alt=media" alt=""><figcaption></figcaption></figure>

When asked to choose a setting, select "From Scratch".

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-a333e1a85b622da96c78a56862ba33a5b987ef3d%2Fimage%20(131).png?alt=media" alt=""><figcaption></figcaption></figure>

**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:

* Low Coverage
  * Coverage Rate below 200x

1. Select the necessary input files for the run, including sample inputs (.fastq.gz, .fastq.ora, .bam, or .cram files), and a Target BED File.
2. Select a reference genome.
3. Map Align Options
   1. Select "Enable Map/Align".
4. (Optional) Variant Calling Options
   1. Select "Enable Small Variant Caller".
5. (Optional) SV Caller Options
   1. Enable SV Calling\ <mark style="color:blue;">**NOTE**</mark>: SV Calling for Enrichment is an experimental feature.
6. Methylation Options
   1. Select "Enable 5-Base Methylation-Aware Algorithms".
7. Start the analysis


---

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