> 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/cloud-analysis-settings.md).

# Cloud Analysis Settings

Overview of DRAGEN Secondary Analysis and Cloud Analysis Settings

### Illumina TruPath Genome DRAGEN Germline Workflow

When proximity mode is enabled, the DRAGEN Germline pipeline supports secondary analysis of TruPath sequencing data, leveraging proximity data to perform the following:

* Provide phased small variant calls and ultra-long phasing blocks, resolving haplotypes
* Resolve mapping ambiguities in challenging regions of the genome, including regions of high homology and segmental duplications
* Provide enhanced structural variant insights using colocation detection

<figure><img src="https://2122546113-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FCiFAstZpxWHpI6k3vTvF%2Fuploads%2Fgit-blob-57ffca5a19e2d2bb1fa3cdc2c02cbabb5361ab5c%2FDragen%20user%20guide%20workflow-v3.jpg?alt=media" alt=""><figcaption></figcaption></figure>

#### Basespace Run Planning / Autolaunch Settings

The DRAGEN Germline pipeline application accessed via BaseSpace Sequence Hub (BSSH) Autolaunch [described in this section here](#illumina-trupath-genome-dragen-germline-workflow) performs the following settings for each variant, including the following per each category:

* **None:** Performs Map/Align by enabling proximity mode.
* **Small Variant Callers:** Enables associated proximity mode callers, including:
  * Targeted Callers (enables a subset of targeted callers)
* **All Variant Callers:** Enables associated proximity mode callers listed in Small Variant Callers category, and:
  * Multi-Region Joint Detection (MRJD) calling on default genes.
  * Copy Number Variant (CNV) calling
  * Structural Variant Calling
  * Short Tandem Repeats (STR) calling

#### Basespace Application and Platform Core Pipeline Settings

The DRAGEN Germline pipeline may be accessed via BaseSpace Appllication or in Platform Core. Both perform the following settings for each variant, including the following per each category:

* Performs Map/Align by enabling proximity mode.
* Small Variant Calling, with option to enable personalization
* Copy Number Variant (CNV) Calling, including CNV related settings
* Structural Variant Calling and related settings
* Short Tandem Repeats (STR) Calling with phasing
* Targeted Callers, including `lpa`, `hba`, and `smn`


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