# DRAGEN Germline Whole Genome

<figure><img src="/files/wYwFXuNveFICtZViv1y4" alt=""><figcaption></figcaption></figure>

Select the DRAGEN\_Germline\_Whole\_Genome\_4-4-6 Pipeline.

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

1. Select the necessary input files for the run, including sample inputs (.fastq, .fastq.ora, .bam, or .cram files), and a custom DRAGEN Reference Genome.
   1. Note: 5-base is compatible with any methyl\_cg references. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.<br>

      <figure><img src="/files/qd2ZhWzTiBDI338BogcO" alt=""><figcaption></figcaption></figure>
2. To Enable Methylation Aware Algorithms, select "True" for Enable 5-Base Methylation-Aware Algorithms.<br>

   <figure><img src="/files/zU9A6pfSzXLBv5TPyqBd" alt=""><figcaption></figcaption></figure>
3. (Optional) To perform Small Variant Calling, set Enable Variant Caller to "True" and Emit Ref Confidence to "GVCF".<br>

   <figure><img src="/files/KWj30QWoVySPFwDRJWPs" alt=""><figcaption></figcaption></figure>
4. If no Small Variant Calling is needed, set Enable Variant Caller to "False" and click the "X" next to Emit Ref Confidence (screenshot displays the button to click; the box will disappear upon selecting).\ <br>

   <figure><img src="/files/xNCuELN3DXOiAolmxDR7" alt=""><figcaption></figcaption></figure>
5. For Report Methylation at Variant Positions, select "default".<br>

   <figure><img src="/files/ODlTYIrh9pMAn9hsY2uX" alt=""><figcaption></figcaption></figure>
6. (Optional) To perform CNV calling, set Enable CNV Calling to "True". Make Sure Enable Allel-Specific CNV Calling is "False".\
   ![](/files/QbPksZvVnmcDd1eGgFti)
7. (Optional) To Enable SV Calling, select "True".
   1. <mark style="color:blue;">**NOTE**</mark>: SV results are turned on to improve CNV calling accuracy, but these results are not verified or supported.

      <figure><img src="/files/4EUro3cJJL9q8TVdVFlD" alt=""><figcaption></figcaption></figure>
8. In the Additional Options section:
   1. (Optional) If downsampling is required, add `--enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads`.

      <figure><img src="/files/Ow4leSpwQaBKY6s4x7Ik" alt=""><figcaption></figcaption></figure>
9. Start the analysis.


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