Option A: Launch from Run Planner

Use this option when you are planning a new sequencing run and want the variant calling pipeline to launch automatically after sequencing completes.

Step-by-Step Instructions

1. Navigate to BaseSpace Sequence Hub (BSSH) and select your desired workgroup. Log in to your domain first if required.

2. Go to the Runs tab, select New Run, then select Run Planning.

3. Set the Analysis Location to BaseSpace/Illumina Connected Analytics.

4. Select DRAGEN somatic for IDT Custom Panels v4.5.4 from the Application drop-down menu.

5. Select the library prep: xGen cfDNA & FFPE Library Prep.

6. Select the Index adapter kit you are using and click Next.

   
7. In the Configuration: DRAGEN Somatic for IDT Custom Panels - 4.5.4, adjust your read lengths if needed.

8. Input Sample IDs and the appropriate Index IDs for each sample.

   Tip. Click on Sample ID and select Fill down to enumerate your samples automatically.

   
9. Provide your target panel BED file in Analysis settings.

10. Select your reference genome of preference.

    IMPORTANT. The reference genome for your BED file, systematic noise analysis, and variant calling must be exactly the same for optimal results. The system will not raise an error if different reference genomes are used.

11. UMI is enabled by default and can be turned off if preferred.

12. Upload your custom systematic noise file from Stage 1. The system also allows you to choose one of the pre-built systematic noise files from Illumina if you have no custom file.

13. (Optional) Upload an excluded regions BED.

14. In the per-sample configuration, select the sample type:

    • Solid: the default mode for solid samples.

    • Low-quality FFPE: assign this tag to low-quality FFPE samples. See Low-Quality FFPE Mode.

    

IMPORTANT. Auto-launch from Run Planner is optimized exclusively for tumor-only samples. To run tumor-normal analysis, use the BaseSpace Sequence Hub (BSSH) or Illumina Connected Analytics (ICA) application instead. See Option B: Launch from BSSH or ICA.

IMPORTANT. When using the Run Planner UI, samples for systematic noise baseline building and the experimental (tumor) samples must be processed on different flow cells. If you need both on the same flow cell, run BCL Convert from Run Planner first, then launch the Baseline Builder app separately from the BSSH or ICA application.