# DRAGEN Germline

<figure><img src="/files/7Zwt3O5yywEv6WyIZr30" alt=""><figcaption></figcaption></figure>

Select the DRAGEN Germline v4.4.6 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).
   1. (Optional) If performing CNV calling:

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

      ![](/files/UjqM99ct7D5ClHVTtBcb)
   2. If running CNV calling, check "Enabled SV calling"
      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.\
         ![](/files/99y1oUm5NM9S2BC2NQBv)
6. Under Methylation for Illumina 5-Base DNA Prep, check the box for "Enable 5-Base Methylation-Aware Algorithms".\
   ![](/files/UOs1RAFfVxzPhl537b7N)
7. Under Advanced settings, check "Enable Optional Metrics". This will provide GC bias reporting.\
   ![](/files/w7HZIwMhvRH8o10FHyVb)
8. (Optional) Under Additional DRAGEN Commandline Arguments, add `--enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads` to enable downsampling.\
   ![](/files/GqfZhU0WAsMs4alaNGg5)


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