> 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/additional-information/previous-dragen-app-pipeline-instructions/ica-analysis-setup/dragen-somatic-whole-genome/dragen-somatic-whole-genome.md).
# DRAGEN Somatic (Whole Genome)
**WARNING**: Deviation from these instructions (including adding additional options) may cause pipeline failure.
1. Select the necessary input files for the run, including Tumor and Normal inputs (.fastq, .fastq.ora, .bam, or .cram files) and a Baseline Systematic Noise Filter BED File.
2. Select a reference genome. 5-base is compatible with any methyl\_cg reference. One recommendation is the Homo sapiens \[1000 Genomes] hg38 v5 Pangenome reference.
1. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.
3. To Enable Methylation Aware Algorithms, check the box for Enable 5-Base Methylation-Aware Algorithms.
4. (Optional, if performing tumor-normal analysis only) Set Enable Germline Variant Calling On Normal Sample to "True".
5. For Report Methylation at Variant Positions, select "default".
6. (Optional) To perform Small Variant Calling:
1. Set Enable Small Variant Caller to "True"
2. Set Emit Ref Confidence to "GVCF"
3. Set Enable VCF File Output to "True".
4. Set Enable Germline Tagging to "True".
7. (Optional) To perform Copy Number Variant Calling:
1. Turn on "Enable CNV Calling" and optinally provide additional BED or PoN files.\
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2. Turn off "Enable Cytogenetics" as this is not supported for 5-base.\
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8. (Optional) To perform Structural Variant Calling:
1. Set Enable SV Calling to "True"
2. (Optional) Upload a Custom SV Target BED or Systematic Noise BED
9. In the UMI Options section:
1. Set Enable UMI to false.
2. Click the "X" next to UMI Library Type (screenshot displays the button to click; the box will disappear upon selecting).
3. Click the "X" next to UMI Aware Variant Calling (screenshot displays the button to click; the box will disappear upon selecting).
4. Click the "X" next to Minimum Supporting UMI Reads (screenshot displays the button to click; the box will disappear upon selecting).
10. In the Variant Annotation Options section:
1. Set Enable Variant Annotation to true
11. In the Additional Options section:
1. (Optional) Check "Enable Variant Annotations" to turn on DRAGEN Variant Annotation.
2. (Optional) If downsampling is required, add `--enable-fractional-down-sampler=true --down-sampler-tumor-subsample=$Fraction` under Additional DRAGEN Commandline Arguments, 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.
3. (Optional) If running cfDNA samples, it's recommended to add `--mbias-report-include-overlaps=true` under Additional DRAGEN Commandline Arguments 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.
4. (Optional) Under Additional DRAGEN Commandline Arguments, add `--gc-metrics-enable=true` to enable GC metrics.
12. Start the analysis.
---
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