> 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/ica-analysis-setup/dragen-germline-whole-genome.md).

# DRAGEN Germline Whole Genome

Select the DRAGEN Germline Whole Genome 4.6.2 Pipeline.

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-644c03a36e96cdd21bc3158a44cff83b98bccda4%2Fimage%20(137).png?alt=media" alt=""><figcaption></figcaption></figure>

When asked to choose a setting, select "From Scratch".

<figure><img src="https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-a333e1a85b622da96c78a56862ba33a5b987ef3d%2Fimage%20(131).png?alt=media" alt=""><figcaption></figcaption></figure>

**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.gz, .fastq.ora, .bam, or .cram files), and a 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.
2. Map Align Options
   1. Select "Enable Map/Align".
   2. Select "Enable Duplicate Marking".
3. (Optional) Variant Calling Options
   1. Select "Enable Small Variant Caller".
   2. Select "Enable Personalization".
4. (Optional) CNV Options
   1. Select "Enable CNV Calling".
   2. Select "Enable Allele-Specific CNV Calling".
   3. Unselect "Enable Cytogenetics".
5. (Optional) SV Options

   1. Select "Enable SV Calling".

   <mark style="color:blue;">**NOTE:**</mark> While supported as a standalone feature, enabling SV calling also improves CNV results, so it's recommended to always run SV calling after enabling CNV calling.
6. (Optional) Variant Annotation Options
   1. Select "Enable Variant Annotation".
7. Methylation Options
   1. Select "Enable 5-Base Methylation Mode for Illumina 5-Base DNA Prep".
8. Advanced Options
   1. If downsampling is required, under Additional DRAGEN Command Line Arguments, add `--enable-fractional-down-sampler=true --down-sampler-normal-subsample=$Fraction`, where $Fraction is a value between 0 and 1 representing the proportion of reads to keep.
   2. (Optional) Under Additional DRAGEN Command Line Arguments, add `--gc-metrics-enable=true` to enable GC metrics.
9. Start the analysis.


---

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