# DRAGEN Germline Enrichment

<figure><img src="/files/Yt8bgF0FsA5q6CSyQvs5" alt=""><figcaption></figcaption></figure>

Select the DRAGEN\_Germline\_Enrichment\_4-4-6 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


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