# DRAGEN Somatic
Select the DRAGEN Somatic 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. \[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.\
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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.\
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8. Under Methylation for Illumina 5-Base DNA Prep, check the box for "Enable 5-Base Methylation-Aware Algorithms".\
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9. Under Advanced Settings, uncheck "Enable Small Variant Calling on Normal Samples" (if doing tumor-only analysis) and check "Enable Variant Annotation".
1. Uncheck "Enable Small Variant Calling on Normal Samples" if doing tumor-only analysis.
2. (Default) Check "Enable Small Variant Calling on Normal Samples" if doing tumor-normal analysis.\
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1. If performing tumor-normal analysis, uncheck the box for Germline Tagging.
10. Under Additional DRAGEN Commandline Arguments, add `--vc-systematic-noise-method=max`.
11. (Optional) Under Additional DRAGEN Commandline Arguments, add `--enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads` to enable downsampling.
12. (Optional) Under Additional DRAGEN Commandline Arguments, add `--gc-metrics-enable=true` to enable GC metrics.
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