DRAGEN Germline

Select the DRAGEN Germline v4.4.6 Application.

1. Add "Analysis Name".

2. Select Project to "Save Results To".

3. Add biosamples 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.

4. If performing variant calling, set Pipeline Configuration to "Map/Align + Small Variant Caller". If not performing variant calling, set Pipeline Configuration to "Map/Align".

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

6. (Optional) If performing CNV calling:

   1. Check the box for "Enable CNV Caller"

   2. Uncheck "Output CNV Ref Calls"

   3. Uncheck "Enable Allele-specific CNV Calling"

   
7. (Optional) If performing SV calling:

   1. Check "Enabled SV calling"

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

9. Under Advanced settings, check "Enable Optional Metrics". This will provide GC bias reporting.

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