DRAGEN Somatic

Select the DRAGEN Somatic v4.4.6 Application.

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" 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) 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.