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.

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. Under Methylation for Illumina 5-Base DNA Prep, check the box for "Enable 5-Base Methylation-Aware Algorithms".

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.

      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) 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.

12. (Optional) Under Additional DRAGEN Commandline Arguments, add --enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads to enable downsampling.

    
13. (Optional) Under Additional DRAGEN Commandline Arguments, add --gc-metrics-enable=true to enable GC metrics.