DRAGEN Somatic (Whole Genome)

Select the necessary input files for the run, including Tumor and Normal inputs (.fastq, .fastq.ora, .bam, or .cram files) and a Baseline Systematic Noise Filter BED File.

Select a reference genome. 5-base is compatible with any methyl_cg reference. One recommendation is the Homo sapiens [1000 Genomes] hg38 v5 Pangenome reference.

1. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic. \

   

To Enable Methylation Aware Algorithms, check the box for Enable 5-Base Methylation-Aware Algorithms. \

(Optional, if performing tumor-normal analysis only) Set Enable Germline Variant Calling On Normal Sample to "True". \

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

(Optional) To perform Small Variant Calling:

1. Set Enable Small Variant Caller to "True"

2. Set Emit Ref Confidence to "GVCF"

3. Set Enable VCF File Output to "True".

4. Set Enable Germline Tagging to "True".

   

In the UMI Options section:

1. Set Enable UMI to false.

2. Click the "X" next to UMI Library Type (screenshot displays the button to click; the box will disappear upon selecting).

3. Click the "X" next to UMI Aware Variant Calling (screenshot displays the button to click; the box will disappear upon selecting).

4. Click the "X" next to Minimum Supporting UMI Reads (screenshot displays the button to click; the box will disappear upon selecting).\

   

In the Variant Annotation Options section:

1. Set Enable Variant Annotation to true \

   

In the Additional Options section:

1. (Optional) If downsampling is required, add --enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads.

   

Start the analysis.