> 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/bssh-analysis-setup/dragen-germline.md).

# DRAGEN Germline

<figure><img src="/files/HjFmTWEL8tog3z8Rughr" alt=""><figcaption></figcaption></figure>

Select the DRAGEN Germline v4.5.4 Application.

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

1. Add "Analysis Name".
2. Select Project to "Save Results To".
3. Add biosamples by uploading FASTQs, BAMs, or CRAMs.
   1. <mark style="color:blue;">**NOTE**</mark>: Multiple files can be uploaded at one time as long as the assigned "Sample Sex" value is the same for all samples. For example, if "Auto-Detect" is selected, it is assigned to all samples selected.
4. If performing variant calling, set Pipeline Configuration to "Map/Align + Small Variant Caller". If not performing variant calling, set Pipeline Configuration to "Map/Align".
5. Select a reference, or upload a Custom DRAGEN Reference File (ie. if using mouse samples).
6. (Optional) If performing CNV calling:

   1. Check the box for "Enable CNV Caller"
      1. Uncheck "Output CNV Ref Calls"
      2. (Optional) Check "Enable Allele-specific CNV Calling"

   ![](/files/UjqM99ct7D5ClHVTtBcb)
7. (Optional) If running SV calling:

   1. Check "Enabled SV calling"

   <mark style="color:$primary;">**NOTE**</mark><mark style="color:$primary;">:</mark> While supported as a stand alone feature, enabling SV calling also improves CNV results, so it's recommended to always run SV calling after enabling CNV calling.\
   ![](/files/99y1oUm5NM9S2BC2NQBv)
8. Under Methylation for Illumina 5-Base DNA Prep, check the box for "Enable 5-Base Methylation-Aware Algorithms".\
   ![](/files/UOs1RAFfVxzPhl537b7N)
9. (Optional) Under Advanced Settings, check "Enable Variant Annotation" to turn on Nirvana Variant Annotations.
10. (Optional) Under Additional DRAGEN Commandline Arguments, add `--enable-fractional-down-sampler=true --down-sampler-normal-subsample=$Fraction` to enable downsampling, where $Fraction is a value between 0 and 1 representing the proportion of reads to keep.
11. (Optional) Under Additional DRAGEN Commandline Arguments, add `--gc-metrics-enable=true` to enable GC metrics.<br>


---

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