Amplicon BED File

The DRAGEN Amplicon Pipeline requires an amplicon BED file and all input files required by the DRAGEN DNA pipeline. Each row in an amplicon BED file describes an amplicon target. The following fields are required.

Field	Description
chrom	The name of the chromosome.
chromStart	The 0-based inclusive start position of the target, excluding the primer.
chromEnd	The 0-based exclusive end position of the target, excluding the primer.
name	The name of the amplicon target.
gene	[Optional] The gene ID.
targetType	[Optional] The target type.

The default segmentation of DNA amplicon mode in copy number variant calling is bed, and can be modified using --cnv-segmentation-mode. The CNV segmentation bed is gene-level and auto-generated based on the gene ID column in the amplicon BED file. In RNA amplicon mode, targetType is used to identify fusion targets where targetType is Fusion. The gene IDs for fusion targets are collected and written to an output file. The default value of --rna-gf-enriched-genes is then set to this file containing fusion gene IDs. A candidate fusion is required to have both partner genes in the gene list. Base-level and read-level coverage is calculated for each region in the amplicon BED file. It is recommended that the fusion targets are commented to avoid competition with gene expression targets.