# DRAGEN Germline Whole Genome

Select the DRAGEN\_Germline\_Whole\_Genome\_4-4-6 Pipeline. **WARNING**: Deviation from these instructions (including adding additional options) may cause pipeline failure. 1. Select the necessary input files for the run, including sample inputs (.fastq, .fastq.ora, .bam, or .cram files), and a custom DRAGEN Reference Genome. 1. Note: 5-base is compatible with any methyl\_cg references. A graph reference is recommended for Germline and non-graph is the recommendation for Somatic.

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

3. (Optional) To perform Small Variant Calling, set Enable Variant Caller to "True" and Emit Ref Confidence to "GVCF".

4. If no Small Variant Calling is needed, set Enable Variant Caller to "False" and click the "X" next to Emit Ref Confidence (screenshot displays the button to click; the box will disappear upon selecting).\

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

6. (Optional) To perform CNV calling, set Enable CNV Calling to "True". Make Sure Enable Allel-Specific CNV Calling is "False".\ ![](https://707781091-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FL2tTN7buOERM9NKPYYlg%2Fuploads%2Fgit-blob-009444b747ae17e7c3c7e23bb8d9a6ef026627b3%2Fimage%20$4$%20$3$.png?alt=media) 7. (Optional) To Enable SV Calling, select "True". 1. **NOTE**: SV results are turned on to improve CNV calling accuracy, but these results are not verified or supported.

8. In the Additional Options section: 1. (Optional) If downsampling is required, add `--enable-down-sampler=true --down-sampler-fragments=$Number_of_Reads`.

9. Start the analysis.