DRAGEN Enrichment App in BaseSpace

DRAGEN Enrichment BaseSpace App Page.

DRAGEN Enrichment BaseSpace v4.5 App Product Guide Page.

Demo Data project "DRAGEN Enrichment Demo" can be found in Public Data.

App use: Perform alignment with the DRAGEN Aligner and variant calling with the DRAGEN variant caller. The App will perform germline or somatic variant calling and optional Copy Number Variants and Structural Variants variant calling.

Versions: 4.2.4 - 4.5.4 are currently available. Illumina recommends using the latest version. All current versions include an Additional Arguments section where a user can enter command-line options to run with the App.

General App Information

Required input

1. A minimum number of reads is not required. However, use sufficient data for each sample to support an appropriate depth of coverage for variant calling.

2. Each analysis uses one target region BED file. Several existing panels are available in the Target Regions drop-down. If using a custom/third party panel, select custom. The BED file must be uploaded prior to app analysis set up.

3. Samples are all paired-end or all single-end.

4. A maximum of 96 samples per analysis.

5. A maximum of 48 BAM or CRAM files per analysis.

Optional Input

1. BAM/CRAM (not required but can be used instead of FASTQs.)

2. Custom reference genome (if pre-built with DRAGEN Reference Builder App). The app requires the tar.gz generated by the DRAGEN Reference Builder app and the FASTA reference file.

3. CNV Baseline files or a Combined Targeted Calling Panel of Normals file (if performing CNV calling with a Panel of Normals, which can be generated using the DRAGEN Baseline Builder application with CNV setup). An In-Run Panel of Normals can be selected alternatively to enable CNV calling.

   1. Normal sample recommendations include samples that underwent the same library preparation, same sequencing platform and are copy normal (known to not have copy number variation).

4. Up to three BED files for for calculating enrichment metrics.

5. Custom Systematic Noise BED file for Somatic variant calling analysis

Analysis Output

1. BAM Files: Aligned sequences and quality scores in the BAM (*.bam) file format.

2. VCF Files: Variant calls in the VCF (*.vcf.gz) file format.

3. Genome VCF Files: Variants, references, and no calls for all sites in the genome VCF (gVCF) file format.

4. Summary File: Statistics for each sample.

Additional Settings

1. Base Padding: default is 0 and 150 (bp) for variant calling and calculating enrichment metrics respectively, however, users have the option to enter whatever value they chose, from 0-10000.

2. 5-Base and UMI library support.

3. Low-pass and high coverage modes.

4. Allele-specific CNV calling (not ideal for small panels).

5. HLA allele typing.

6. CheckFingerprint (germline only)

7. Contamination detection (optional for somatic mode, runs by default for germline mode)

8. Biomarkers support for somatic variant calling: TMB and Fragmentomics (Other biomarker analysis can be enabled but not recommended)

9. Variant Annotation for somatic variant calling.

10. Many other input form options and Additional Arguments section.

For any feedback or questions regarding this article (Illumina Knowledge Article #3686), contact Illumina Technical Support [e-mail].