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
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_Heme_dir
Folder Structure on ICAcustom_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

Last updated
Was this helpful?