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          • ROH Caller
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          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
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          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
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          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
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        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
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        • DUX4 Rearrangement Caller
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        • Splice Variant Caller
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On this page
  • Local App Setup
  • Overview
  • Customization with customConfig and customResourceDir
  • Important note for using File Parameters
  • Examples
  • Command Line
  • heme_custom_param.config Content
  • custom_resources_Heme_dir Folder Structure
  • customConfig Template (with default value)
  • Supported Parameters

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  1. Product Guides
  2. DRAGEN v4.4
  3. Clinical Research Workflows
  4. DRAGEN Heme WGS Tumor Only Pipeline
  5. DRAGEN Server App
  6. Advanced Topics

Custom Config Support

Local App Setup

Overview

This document describes how to use the Custom Configuration Support feature for the pipeline software. This feature allows users to customize a specific set of DRAGEN command-line options to override the default values pre-defined in the pipeline.

Customization with customConfig and customResourceDir

Users can customize pipeline behavior and file inputs using:

  • --customConfig : path to a custom configuration file listing customized parameter values.

  • --customResourceDir : path to a directory containing custom resource files.

Both options should be used together if file-based overrides are required.

Important note for using File Parameters

  • For file parameters (parameters that require a file), users must specify relative paths in the customConfig file. The software will join customResourceDir and the relative path to form the full file path.

  • Additionally, the value assigned to a file parameter must be enclosed in single quotes ('').

Examples

Command Line

run_Heme_WGS_TO_4.4.4.x.sh \
  --inputType bcl \
  --inputFolder /heme_input_bcl \
  --customConfig /path/heme_custom_param.config \
  --customResourceDir custom_resources_Heme_dir

heme_custom_param.config Content

## custom parameters
vc_output_evidence_bam = false
qc_detect_contamination = true
aligner_clip_pe_overhang = 0

## custom reference files
vc_systematic_noise = '/snv/WGS_hg38_v1.0_systematic_noise.snv.bed.gz'
sv_systematic_noise = '/sv/WGS_FF_Heme_hg38_v1.0_systematic_noise.sv.bedpe.gz'
vc_somatic_hotspots = '/snv/somatic_hotspots_GRCh38.vcf.gz'

custom_resources_Heme_dir Folder Structure

custom_resources_Heme/
├── snv
│   ├── WGS_hg38_v1.0_systematic_noise.snv.bed.gz
│   └── somatic_hotspots_GRCh38.vcf.gz
└── sv
    └── WGS_FF_Heme_hg38_v1.0_systematic_noise.sv.bedpe.gz

customConfig Template (with default value)

#vc_systematic_noise = ''
#enable_map_align = true
#sv_systematic_noise = ''
#vc_output_evidence_bam = false
#qc_detect_contamination = true
#vc_somatic_hotspots = ''
#sv_somatic_ins_tandup_hotspot_regions_bed = ''
#cram_reference = ''
#aligner_clip_pe_overhang = 0

Supported Parameters

Display Name
Parameter Name
Component
Allowed Values
Default Value
Optional

VC Systematic Noise File

vc_systematic_noise

Variant Caller

file

included

Yes

VC Somatic Hotspots File

vc_somatic_hotspots

Variant Caller

file

included

Yes

CRAM Input Reference Genome

cram_reference

Mapper

file

included

Yes

Aligner Clip Paired End Reads Overhang

aligner_clip_pe_overhang

Mapper

0,1,2

0

Yes

Enable Map Align

enable_map_align

Mapper

true / false

true

Yes

SV Somatic Hotspot BED File

sv_somatic_ins_tandup_hotspot_regions_bed

Structural VC

file

included

Yes

SV Systematic Noise File

sv_systematic_noise

Structural VC

file

included

Yes

Output SNV Evidence BAM

vc_output_evidence_bam

Debug

true / false

false

Yes

QC Detect Contamination

qc_detect_contamination

QC

true / false

true

Yes


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