Custom Config Support

This feature allows users to customize a specific set of DRAGEN command-line options to override the default values pre-defined in the pipeline.

ICA Setup

On the ICA (Illumina Connected Analytics) user interface (UI) to the software, you can specify the Custom Parameters Config File and Custom Resources Directory directly. Supported customizable options are described below.

Examples

solid_custom_param.config Content

## custom parameters
somatic_vc_output_evidence_bam = false
germline_qc_detect_contamination = true
germline_aligner_clip_pe_overhang = 0

## custom reference files
somatic_sv_systematic_noise = '/snv/WGS_hg38_v1.0_systematic_noise.snv.bed.gz'
somatic_sv_systematic_noise = '/sv/WGS_FF_solid_hg38_v1.0_systematic_noise.sv.bedpe.gz'
somatic_vc_somatic_hotspots = '/snv/somatic_hotspots_GRCh38.vcf.gz'

custom_resources_Heme_dir Folder Structure on ICA

custom_resources_Solid/
├── snv
│   ├── WGS_Solid_hg38_v1.0_systematic_noise.snv.bed.gz
│   └── somatic_hotspots_GRCh38.vcf.gz
└── sv
    └── WGS_Solid_FF_solid_hg38_v1.0_systematic_noise.sv.bedpe.gz

ℹ️ Note: Custom resource files and the custom configuration file must be uploaded to the same ICA project where the run is created. You can use the icav2 client or other supported methods. See Data Transfer Options with ICA Platform for details.

ICA Input Files UI Example

ICA Setup Screenshot