> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/illumina-trupath-genome/run-analysis-setup/basespace-analysis.md).

# Basespace Analysis

This section describes the steps required to execute the DRAGEN Germline for TruPath analysis via Basespace Application.

## Launch DRAGEN Germline from the BaseSpace App

In Basespace, select the latest DRAGEN Germline App version. In this example, 4.5.4 is shown.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-9d0c79db6ef4861e01d5d3bd02318a089880fb5a%2Fscreen1.png?alt=media" alt=""><figcaption></figcaption></figure>

1\. In BaseSpace Sequence Hub, open Apps and select DRAGEN Germline.

2\. Under Input Data, choose Biosamples (FASTQs across multiple runs).

3\. Name the analysis, select the destination project, and choose your biosample FASTQs.

4\. Set Pipeline Configuration to Map/Align + Small Variant Caller.

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-9da4b1dce6a19d2b1cdc9b74d9df27d09167f231%2Fscreen2.png?alt=media" alt=""><figcaption></figcaption></figure>

5\. Select the following settings, as shown above:

* Map/Align — BAM output, duplicate marking enabled
* Small Variant Caller — VCF and GVCF, personalization enabled
* CNV — enabled with self-normalization

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-467a84b0c5f07a46b0d0ac385e73c8f0702c9ddd%2Fscreen3.png?alt=media" alt=""><figcaption></figcaption></figure>

6\. Select the following settings, as shown above:

* SV — Enable SV Caller
* STR — Enable STR Caller (Default with SMN)
* <mark style="color:$warning;">**REQUIRED:**</mark>**&#x20;Illumina TruPath Genome Options — Enable Proximity Mode and Enable MRJD Caller**
* Targeted Callers — Enable Targeted callers\
  (HLA Calling is currently not supported with TruPath. Additioanl Star Allele Calling options can be provided in the additional arguments section.)

7. Select to Launch, and monitor under Analyses. When analysis completes, open the results in your project to review outputs.


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