> 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/additional-information/previous-dragen-app-pipeline-instructions/ica-analysis-setup/dragen-germline-enrichment.md).
# DRAGEN Germline Enrichment
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.
4. For Report Methylation at Variant Positions, select "default".
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
6. Start the analysis
---
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