# 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>

#### BSSH Run Planning / Autolaunch Settings

The DRAGEN Germline pipeline application accessed via BaseSpace Sequence Hub (BSSH) Autolaunch [described in this section here](https://help.connected.illumina.com/illumina-trupath-genome/sequencing-run-setup/novaseq-x-run-planning-dragen-germline) 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

#### ICA Pipeline Settings

The DRAGEN Germline pipeline application accessed via BaseSpace Sequence Hub (BSSH) Autolaunch [described in this section here](https://help.connected.illumina.com/illumina-trupath-genome/run-analysis-setup/ica-analysis) performs 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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