DRAGEN
Illumina Connected Software
  • Overview
    • Illumina® DRAGEN™ Secondary Analysis
    • DRAGEN Applications
    • Deployment Options
  • Product Guides
    • DRAGEN v4.4
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • Clinical Research Workflows
        • DRAGEN Heme WGS Tumor Only Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
        • DRAGEN Solid WGS Tumor Normal Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Quick Start
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
            • Custom Workflow
              • Custom Config Support
            • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • Illumina scRNA
        • Other scRNA prep
        • RNA Panel
        • RNA WTS
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Pedigree Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • Available pipelines
            • Germline CNV Calling (WGS/WES)
            • Germline CNV Calling ASCN (WGS)
            • Multisample Germline CNV Calling
            • Somatic CNV Calling ASCN (WGS)
            • Somatic CNV Calling WES
            • Somatic CNV Calling ASCN (WES)
          • Additional documentation
            • CNV Input
            • CNV Preprocessing
            • CNV Segmentation
            • CNV Output
            • CNV ASCN module
            • CNV with SV Support
            • Cytogenetics Modality
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
          • Structural Variant IGV Tutorial
        • VNTR Calling
        • Population Genotyping
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • JSON Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single Cell Pipeline
        • Illumina PIPseq scRNA
        • Other scRNA Prep
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN MRD Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
        • Docker Requirements
      • DRAGEN Reports
      • Tools and Utilities
    • DRAGEN v4.3
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • CNV Output
          • CNV with SV Support
          • Multisample CNV Calling
          • Somatic CNV Calling WGS
          • Somatic CNV Calling WES
          • Allele Specific CNV for Somatic WES CNV
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
        • VNTR Calling
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
          • Effective Coverage Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single-Cell Pipeline
        • scRNA
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • RNA Panel
        • RNA WTS
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
      • DRAGEN Reports
      • Tools and Utilities
  • Reference
    • DRAGEN Server
    • DRAGEN Multi-Cloud
      • DRAGEN on AWS
      • DRAGEN on AWS Batch
      • DRAGEN on Microsoft Azure
        • Run DRAGEN VM on Azure
      • DRAGEN on Microsoft Azure Batch
        • Azure Batch Run Modes
    • DRAGEN Licensing
      • DRAGEN Server Licensing
      • DRAGEN Cloud Licensing
    • DRAGEN Application Manager
    • Support
    • Resource Files
      • Noise Baselines
    • Supplementary Information
    • Troubleshooting
    • Citing DRAGEN software
    • Release Notes
    • Revision History
Powered by GitBook
On this page
  • Overview
  • Functionality
  • Prerequisites
  • Basic usage
  • Input files and command line options
  • Output format

Was this helpful?

Export as PDF
  1. Product Guides
  2. DRAGEN v4.4
  3. DRAGEN DNA Pipeline

DUX4 Rearrangement Caller

Overview

The DUX4 Rearrangement Caller identifies the events of potential structural rearrangements between DUX4 and other genes (including IGH).

Functionality

The DUX4 Rearrangement Caller has the following features:

  • call DUX4 Rearrangement events from various format of genomic data like FASTQ, BAM, CRAM.

  • scan the whole genome and identify potential DUX4 rearrangement events.

  • run in parallel with the host DRAGEN software with minimal overhead.

Prerequisites

  • Sequencing dataset to be tumor-only, paired-end and whole-genome sequencing

  • Sequencing dataset with mean coverage range between 25X to 120X

  • Sequencing dataset with mean fragment length between 300 to 500bp

  • Sequencing dataset with mean read length between 100 to 151bp

  • A human reference genome of version hg38

  • A human reference genome of the format that is compatible with DRAGEN software. You can download prebuilt reference genomes from our website or build your own customized version with: dragen --build-hash-table true --output-directory <HASHTABLE_DIR> --ht-reference <REF_FASTA> [options]

The DRAGEN DUX4 caller has been validated with a cohort of samples that fall within the above defined parameters. If you have datasets that don't comply with the above parameters, you can bypass the requirements check by specifying --dux4-skip-santiy-check true to obtain experimental results.

Basic usage

The basic syntax of the DRAGEN command line is:

dragen [global options] [pipeline options] [output options]

  • The global options are common to all pipelines and control the general behavior of DRAGEN, such as the input and output files/directories, the reference genome, and the license file.

  • The pipeline options are specific to each pipeline and control the parameters and features of the analysis, such as the variant callers, the filters and the annotations.

  • The output options control the format and content of the output files, such as the VCF, BAM, and the metrics files.

Input files and command line options

For DUX4 caller, a simple and quick example would be:

dragen \
-r ${HASHTABLE_DIR} \
--enable-map-align=true \
--enable-sort=true \
--enable-duplicate-marking=true \
--tumor-fastq1 test_IGH_DUX4.bam.r1.fastq \
--tumor-fastq2 test_IGH_DUX4.bam.r2.fastq \
--enable-dux4-caller=true \
--output-dir=${OUT_DIR} \
--output-file-prefix=${OUTPUT_PREFIX}

where DRAGEN analysis will take in sequencing data from fastq format (BAM, CRAM, ORA also acceptable) and map/align the reads to the reference genome, the mapped and sorted reads will be consumed by DUX4 caller.

Alternatively, DRAGEN DUX4 caller can start from bam format input by skipping the map/align step (assuming bam file is sorted and with duplicates being marked):

dragen \
-r ${HASHTABLE_DIR} \
--enable-map-align=false \
--tumor-bam-input test_IGH_DUX4.bam \
--enable-dux4-caller=true \
--output-dir=${OUT_DIR} \
--output-file-prefix=${OUTPUT_PREFIX}

What's more, DUX4 caller can run in parallel with other variant callers:

dragen \
-r ${HASHTABLE_DIR} \
--enable-map-align=true \
--enable-sort=true \
--enable-duplicate-marking=true \
--tumor-fastq1 test_IGH_DUX4.bam.r1.fastq \
--tumor-fastq2 test_IGH_DUX4.bam.r2.fastq \
--enable-dux4-caller=true \
--enable-sv=true \
--enable-variant-caller=true \
--output-dir=${OUT_DIR} \
--output-file-prefix=${OUTPUT_PREFIX}

Finally, you will find DUX4 VCF results in the directory of --output-dir with prefix being specified by --output-file-prefix.

Output format

The DUX4 VCF will contain positive calls that represent translocation events across gene pairs. Each event will consist of a set of 4 VCF Breakend records to describe the potential translocation event. Each record will contain PR:SR:SRPB tags to describe the number of fragment that support the events, where PR stands for number of spanning paired reads, SR stands for number of spanning split reads and SRPB stands for number of support read pairs per billion reads being processed. We predefined two sets of genomics target regions, "CoreDUX4" regions and "ExtendedDUX4" regions, to optimize the events detection process, where "CoreDUX4" regions is a subset of "ExtendedDUX4" regions. To avoid potentially duplicated calls, a "CoreDUX4Present" filter label can be assigned to records that are from ExtendedDUX4 regions depending on if there exists any records that are from the corresponding CoreDUX4 regions.

An output VCF example will look like this:

##FILTER=<ID=CoreDUX4Present,Description="Event called from ExtendedDUX4 regions is redundant if another event called from CoreDUX4 regions is present">
##INFO=<ID=TotalReadsNum,Number=1,Type=Integer,Description="Total number of reads for SRPB normalization">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed">
##FORMAT=<ID=SRPB,Number=.,Type=FLOAT,Description="Supporting read pairs per billion">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample001
chr3    75667931        ExtendedDUX4:IGH:Bnd_W  T       T[chr14:105586938[      .       CoreDUX4Present SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=ExtendedDUX4:IGH:Bnd_X;TotalReadsNum=1837703714       GT:PR:SR:SRPB   1/1:.,129:.,42:93.05
chr3    75667932        ExtendedDUX4:IGH:Bnd_V  G       ]chr14:105586937]G      .       CoreDUX4Present SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=ExtendedDUX4:IGH:Bnd_U;TotalReadsNum=1837703714       GT:PR:SR:SRPB   1/1:.,129:.,42:93.05
chr4    190020407       CoreDUX4:IGH:Bnd_W      C       C[chr14:105586938[      .       PASS    SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=CoreDUX4:IGH:Bnd_X;TotalReadsNum=1837703714   GT:PR:SR:SRPB   1/1:.,128:.,42:92.51
chr4    190020408       CoreDUX4:IGH:Bnd_V      C       ]chr14:105586937]C      .       PASS    SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=CoreDUX4:IGH:Bnd_U;TotalReadsNum=1837703714   GT:PR:SR:SRPB   1/1:.,128:.,42:92.51
chr14   105586937       CoreDUX4:IGH:Bnd_U      T       T[chr4:190020408[       .       PASS    SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=CoreDUX4:IGH:Bnd_V;TotalReadsNum=1837703714   GT:PR:SR:SRPB   1/1:.,128:.,42:92.51
chr14   105586937       ExtendedDUX4:IGH:Bnd_U  T       T[chr3:75667932[        .       CoreDUX4Present SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=ExtendedDUX4:IGH:Bnd_V;TotalReadsNum=1837703714       GT:PR:SR:SRPB   1/1:.,129:.,42:93.05
chr14   105586938       CoreDUX4:IGH:Bnd_X      A       ]chr4:190020407]A       .       PASS    SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=CoreDUX4:IGH:Bnd_W;TotalReadsNum=1837703714   GT:PR:SR:SRPB   1/1:.,128:.,42:92.51
chr14   105586938       ExtendedDUX4:IGH:Bnd_X  A       ]chr3:75667931]A        .       CoreDUX4Present SVTYPE=BND;CIPOS=.,.;EVENTTYPE=TRA;MATEID=ExtendedDUX4:IGH:Bnd_W;TotalReadsNum=1837703714       GT:PR:SR:SRPB   1/1:.,129:.,42:93.05
PreviousPopulation Haplotyping (Beta)NextDRAGEN RNA Pipeline

Last updated 2 days ago

Was this helpful?