# 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.

   <figure><img src="/files/Kk44c9qOPac1M48ndBDU" alt=""><figcaption></figcaption></figure>
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](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md).
8. Provide the **systematic noise file** generated in [Stage 1](/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/noise-baseline.md).
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.

    <figure><img src="/files/nrZMjFo0J2nkT7XiDQHV" alt=""><figcaption></figcaption></figure>
13. Launch the analysis.

{% hint style="warning" %}
**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.
{% endhint %}


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