# 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**.

   <figure><img src="/files/ukciX7UQx9irK5NDmwNc" alt=""><figcaption></figcaption></figure>
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.

   <div data-gb-custom-block data-tag="hint" data-style="info" class="hint hint-info"><p><strong>Tip.</strong> Click on <strong>Sample ID</strong> and select <strong>Fill down</strong> to enumerate your samples automatically.</p></div>

   <figure><img src="/files/MbI1gmmxwzBGm5Tmal12" alt=""><figcaption></figcaption></figure>
9. Provide your **target panel BED file** in Analysis settings.
10. Select your reference genome of preference.

    <div data-gb-custom-block data-tag="hint" data-style="warning" class="hint hint-warning"><p><strong>IMPORTANT.</strong> The reference genome for your BED file, systematic noise analysis, and variant calling must be <strong>exactly the same</strong> for optimal results. The system will not raise an error if different reference genomes are used.</p></div>
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](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md).

    <figure><img src="/files/1Rp1hQ7zOUxFsO6DbmQ5" alt=""><figcaption></figcaption></figure>

{% hint style="warning" %}
**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](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-b-bssh-ica.md).
{% endhint %}

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


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-a-run-planner.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.