> 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-somatic.md).
# DRAGEN Somatic
Select the DRAGEN Somatic 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. \[Default] Pipeline Configuration should be "Map/Align + Somatic Small Variant Caller (FASTQ or BAM or CRAM input)".
4. Somatic CNV Calling is "None" by default. Optionally, select "Tumor-only" or "Tumor-Normal" depending on the input type.\
5. Add tumor biosamples by uploading FASTQs, BAMs, or CRAMs. Optionally, add normal samples by uploading FASTQs, BAMs, or CRAMs.
1. **NOTE**: 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.
6. Select a reference.
7. \[Default] Check "Enable Systematic Noise Filter" and select the relevant data file.\
8. (Optional) If performing SV calling, turn on "Enable SV calling" and provide optional custom SV target beds and custom noise files.\
\
9. Under Methylation for Illumina 5-Base DNA Prep, check the box for "Enable 5-Base Methylation-Aware Algorithms".\
10. Under Advanced Settings:
1. Uncheck "Enable Small Variant Calling on Normal Samples" (if doing tumor-only analysis)
2. Uncheck "Enable Small Variant Calling on Normal Samples" if doing tumor-only analysis.
3. (Optional) Check "Enable Variant Annotation" to turn on Nirvana Variant Annotations.
4. (Optional) Check "Enable Small Variant Calling on Normal Samples" if doing tumor-normal analysis.\
\
5. If performing tumor-normal analysis, uncheck the box for Germline Tagging.
11. Under Additional DRAGEN Commandline Arguments, add `--vc-systematic-noise-method=max`.
12. (Optional) If running cfDNA samples, it's recommended to add `--mbias-report-include-overlaps=true` to ensure the M-bias report captures the full R2 read-cycle profile. This is important for cfDNA since the short fragments cause most of R2 to overlap R1 and be excluded from bias statistics by default.
13. (Optional) Under Additional DRAGEN Commandline Arguments, add `--enable-fractional-down-sampler=true --down-sampler-tumor-subsample=$Fraction` to enable downsampling, where $Fraction is a value between 0 and 1 representing the proportion of reads to keep. For tumor-normal analyses, use `--down-sampler-normal-subsample` for the normal sample.
14. (Optional) Under Additional DRAGEN Commandline Arguments, add `--gc-metrics-enable=true` to enable GC metrics.
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