DRAGEN Enrichment App in BaseSpace

DRAGEN Enrichment BaseSpace App Page.

DRAGEN Enrichment BaseSpace App Help Page.

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: 3.4.5 - v3.10.4. Illumina recommends using the latest version. v3.6.3 and above includes an Additional Arguments section where a user can enter command-line options to run with the App.

General App Information

Required input

1. The minimum read length is 50 bases.

2. 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.

3. Each analysis uses one target region BED. The BED file for target region must be sorted by chromosome and start location. 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.

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

5. Sample FASTQ files must already be adapter trimmed.

6. A maximum of 96 samples per analysis.

7. 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 (if performing CNV calling, must come from DRAGEN CNV Baseline Builder.)

   1. Baseline files should come from samples that underwent the same library preparation and are copy normal (known to not have copy number variation).

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.

See the complete list of output files here.

Additional Settings

1. Base Padding: default/recommendation is 150 (bp), however, users have the option to enter whatever value they chose, from 0-10000. This value is used to calculate enrichment metrics.

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