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

# DRAGEN Germline

Select the DRAGEN Germline v4.6.2 application.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-173b2d6174888d673db6a26ce8e65e2698892daf%2Fimage%20(21).png?alt=media" alt=""><figcaption></figcaption></figure>

**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.
6. (Optional) Provide a Target BED for Small Variant Caller.
7. Map/Align Options
   1. Ensure "Enable Duplicate Marking" is selected.
8. (Optional) Small Variant Caller Options
   1. "Enable Personalization" is recommended to improve variant calling.
9. (Optional) CNV Options

   1. Select "Enable CNV Caller"
   2. Select "Enable Allele-specific CNV Calling"

   <mark style="color:blue;">**NOTE**</mark>: It's recommended to enable SV calling when running CNV, as it improves CNV results.
10. (Optional) Structural Variants:
    1. Check "Enabled SV calling"
11. Methylation for Illumina 5-Base DNA Prep
    1. Select "Enable 5-Base Methylation-Aware Algorithms"
12. (Optional) Variant Annotation
    1. Select "Enable Variant Annotation" to turn on DRAGEN Variant Annotations.
13. (Optional) Additional Arguments
    1. Under Additional DRAGEN Command Line 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.
    2. Under Additional DRAGEN Command Line Arguments, add `--gc-metrics-enable=true` to enable GC metrics.<br>


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