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.

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 -

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).

  
• 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).

For any feedback or questions regarding this article (Illumina Knowledge Article #7870), contact Illumina Technical Support [e-mail].