DRAGEN Germline Enrichment

Select the DRAGEN_Germline_Enrichment_4-4-6 Pipeline. This pipeline can traditionally only be run with the low coverage settings, due to the post-collapsed coverage rates required.

Coverage Rate Minimums

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

• Coverage Rate >20x for Germline Methyl-Only

• Coverage Rate >30x for Germline Methyl + VC

1. Select the necessary input files for the run, including sample inputs (.fastq, .fastq.ora, .bam, or .cram files), and a Target BED File.

2. Select a reference genome. 5-base is compatible with any methyl_cg references. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.

3. To Enable Methylation Aware Algorithms, select "True" for Enable 5-Base Methylation-Aware Algorithms. \

   
4. For Report Methylation at Variant Positions, select "default".\

   
5. In the Variant Calling Options section:

   1. Set Emit Ref Confidence to GVCF

   2. Set Enable VCF File Output to true

   3. Set Enable CNV calling to false

   4. Set CNV Enable In-Run Panel of Normals to false

   5. Set CNV GC Bias Correction to false

   6. Set Enable SV calling to false \

      
6. Start the analysis