# Running DRAGEN Amplicon 3.10.4 on BaseSpace on a single sample type with a hg38 reference

The DRAGEN Amplicon app can be used to analyze DNA and RNA Amplicon samples. Information about this pipeline can be found in the [DRAGEN user guide](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/Amplicon_Pipeline.htm).

The latest version of the app, **3.10.4**, has an issue while launching **DNA or RNA samples (not both)** when:

1. A **custom BED file** and **a hg38 reference genome** are selected. The in-built Amplicon manifests were designed for hg19 and can only be used if a hg19 reference is selected in the app.
2. **Nirvana annotation** is **enabled** for **GRCh38.**

For instance when the user select only a DNA sample -

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-97cb2f0964f32bb59d90df3b4d79ada89e01a864%2Fimage1.png?alt=media\&token=8121dd58-c601-43f8-b92e-34cfee4b59c8)

A similar error will be raised if the user only input a RNA sample.

Currently, there are two ways this error can be mitigated:

1. **Disable Nirvana** annotation.
2. Select **'Custom**' for the **Targeted Amplicons input** in **both the DNA and RNA sections** (even if only one type of sample is being analyzed).

* When analyzing **only RNA samples** (with a custom hg38 BED file), select '**Custom**' for the **Targeted Amplicons** input in the **DNA section**, and **choose a BED** file in the '**Custom Manifest File**' section (this can be the same BED file that was used with the RNA samples).

  ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-0c637d7f5c60407ff96b572bad42adbbf89ffd81%2Fimage2.png?alt=media\&token=20998be3-6517-435a-a285-7b6956ab491d)
* If only analyzing **DNA** samples, it would suffice if the user choose '**Custom**' for the **Targeted Amplicons input** in the **RNA section** (not required to actually chose a custom BED file).

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