Option B: Launch from BSSH

Use this option when you have existing data, need tumor-normal analysis, or want more control over the pipeline configuration.

Step-by-Step Instructions

1. If starting from BCL files: First run BCL Convert (from Run Planner or the BCL Convert app) to generate FASTQ files.

2. Open the DRAGEN for IDT Custom Panels application in BaseSpace Sequence Hub (BSSH).

3. Complete the analysis name and select where to save your results.

4. Select your biosamples:

   • Tumor-only: Select your tumor samples from the biosample wizard. You can select any number of samples at a time.

   • Tumor-normal: Select each tumor-normal sample pair one at a time.

   
5. Select your reference genome.

6. UMI is enabled by default. You can turn it off is of preference.

7. Choose the Somatic Sample type.

   1. For samples with low quality (DIN ≤ 2), choose the low-quality FFPE sample type. This enables filters that increase the specificity of variant calls on degraded samples. Note that this may slightly decrease sensitivity. See Low-Quality FFPE Mode.

8. Provide the systematic noise file generated in Stage 1.

9. Upload or select your target panel BED file.

10. (Optional) Upload a block-zone BED file for additional filtering.

11. (Optional) If running normals you can activate Germline variant calling (note that this option will activate charge for an additional sample).

12. All advanced settings have been pre-configured for the IDT xGen cfDNA and FFPE library prep. There is no requirement for customers to modify them unless desired.

    
13. Launch the analysis.

IMPORTANT. The app currently runs in one configuration. If you select the low-quality FFPE sample mode, all samples in that run will be filtered the same way. Therefore, the recommendation is to run low-quality samples in one app session and other solid samples in a separate session.