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        • Prepare a Reference Genome
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        • Read Trimming
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        • 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
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          • De Novo Repeat Expansion Detection
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          • 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
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        • 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
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        • Gene Expression Quantification
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        • Splice Variant Caller
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        • DNA Somatic Tumor-Normal Solid Panel
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        • DNA Somatic Tumor-Normal Solid WES
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  1. Product Guides
  2. DRAGEN v4.3

DRAGEN Recipes

PreviousKmer Classifier Database BuilderNextDNA Germline Panel UMI

Last updated 2 days ago

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Overview

The following sub-pages contain recommended command line options for specific DRAGEN pipelines. For an overview of DRAGEN command line parsing, also see

Germline Pipelines

RNA and scRNA Pipelines

Somatic Pipelines

Multicaller Workflows
DNA Germline Panel UMI
DNA Germline Panel
DNA Germline WES UMI
DNA Germline WES
DNA Germline WGS UMI
DNA Germline WGS
RNA Panel
RNA WTS
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