DRAGEN Enrichment

Select the DRAGEN Enrichment v4.4.6 Application.

Coverage Rate Minimums

The following coverage rates are the minimums recommended for each of the various workflows:

• High Coverage

  • Post-Collapsed Coverage Rate >2000x (liquid tumor mode)

• Medium Coverage

  • Post-Collapsed Coverage Rate 200-300x (solid tumor mode)

• Low Coverage

  • Coverage Rate >20x for Germline Methyl-Only

  • Coverage Rate >30x for Germline Methyl + VC

  • Coverage Rate >100x for Somatic Methyl + VC

If the UMI-collapsed reads do not meet the recommended post-collapsed coverage depths for the solid tumor or liquid biopsy pipelines, then it is recommended to run with the default UMI settings.

1. Add "Analysis Name".

2. Select Project to "Save Results To".

3. Add biosamples by uploading FASTQs, BAMs, or CRAMs.

   1. Sample Sex should be "Auto Detect".

4. If performing somatic variant calling, modify the Variant Caller Mode. If performing Germline Enrichment, keep variant caller mode on "Germline".

5. Select a reference, or upload a Custom DRAGEN Reference File (ie. if using mouse samples).

6. (Optional) Enable targeted regions for a custom BED, and select a custom target BED file.\

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

8. For high coverage samples (Post-Collapsed Coverage Rate >2000x) using Somatic Variant Caller Mode, modify the following settings:

   1. Under Somatic Variant Calling, check "Enable liquid tumor mode" and upload a Baseline Systematic Noise Filter BED file.

   2. Under Somatic Variant Calling, check "Enable Common Germline Variant Tagging".

   3. Under UMI Settings, check "Enable UMI" and set UMI-Aware Variant Calling to "High depth".

   4. Under Advanced Settings, check "Enable Variant Annotation" and "Ignore Overlapping Mates".

   5. Under Additional DRAGEN Commandline Arguments, add --vc-systematic-noise-method=mean.

9. For medium coverage samples (Post-Collapsed Coverage Rate 200-300x) using Somatic Variant Caller Mode, modify the following settings:

   1. Under Somatic Variant Calling, check "Enable liquid tumor mode" and upload a Baseline Systematic Noise Filter BED file.

   2. Under Somatic Variant Calling, check "Enable Common Germline Variant Tagging".

   3. Under UMI Settings, check "Enable UMI", set UMI-Aware Variant Calling to "Low depth", and UMI Min Supported Reads to "1".

   4. Under Advanced Settings, check "Enable Variant Annotation" and "Ignore Overlapping Mates".

   5. Under Additional DRAGEN Commandline Arguments, add --vc-systematic-noise-method=mean.

10. For low coverage samples (Coverage Rate >20x for Germline Methyl-Only; Coverage Rate >30x for Germline Methyl + VC; Coverage Rate >100x for Somatic Methyl + VC) using Somatic Variant Caller Mode, modify the following settings:

    1. Under Somatic Variant Calling, upload a Baseline Systematic Noise Filter BED file.

    2. Under Advanced Settings, check "Ignore Overlapping Mates".

    3. Under Additional DRAGEN Commandline Arguments, add --vc-systematic-noise-method=mean and --enable-duplicate-marketing=true. \