# DRAGEN ## Landing Page - [Illumina® DRAGEN™ Secondary Analysis](https://help.dragen.illumina.com/welcome/welcome-page.md) - [DRAGEN Applications](https://help.dragen.illumina.com/welcome/key-applications.md) - [DRAGEN User Guides](https://help.dragen.illumina.com/welcome/directory.md) - [Deployment Options](https://help.dragen.illumina.com/welcome/deployment-options.md) ## DRAGEN v4.5 - [Illumina® DRAGEN™ Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.5/overview/welcome-page.md) - [DRAGEN Applications](https://help.dragen.illumina.com/dragen-v4.5/overview/key-applications.md) - [Deployment Options](https://help.dragen.illumina.com/dragen-v4.5/overview/deployment-options.md) - [DRAGEN v4.5](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5.md) - [Getting Started](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/getting-started.md) - [DRAGEN Host Software](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-host-software.md) - [DRAGEN Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-host-software/dragen-platform.md) - [DRAGEN Apps](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps.md) - [DRAGEN Germline Enrichment ICA App](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-germline-enrichment-ica-app.md) - [DRAGEN Enrichment BSSH App](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-enrichment-bssh-app.md) - [DRAGEN Germline Enrichment from BCLs BSSH App](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-apps/dragen-germline-enrichment-from-bcls-bssh-app.md) - [DRAGEN Recipes](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes.md) - [DNA Germline Amplicon](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-amplicon.md) - [DNA Germline Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-panel.md) - [DNA Germline Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-panel-umi.md) - [DNA Germline WES](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wes.md) - [DNA Germline WES UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wes-umi.md) - [DNA Germline WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-germline-wgs.md) - [DNA Somatic Tumor-Normal Heme WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-heme-wgs.md) - [DNA Somatic Tumor-Normal MRD](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-mrd.md) - [DNA Somatic Tumor-Normal Solid Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) - [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) - [DNA Somatic Tumor-Normal Solid WES](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) - [DNA Somatic Tumor-Normal Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) - [DNA Somatic Tumor-Normal Solid WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) - [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) - [DNA Somatic Tumor-Only Heme WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) - [DNA Somatic Tumor-Only Solid Amplicon](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-amplicon.md) - [DNA Somatic Tumor-Only Solid Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) - [DNA Somatic Tumor-Only Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) - [DNA Somatic Tumor-Only Solid WES](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) - [DNA Somatic Tumor-Only Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) - [DNA Somatic Tumor-Only Solid WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) - [DNA Somatic Tumor-Only Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) - [DNA Somatic Tumor-Only ctDNA Amplicon](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-ctdna-amplicon.md) - [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) - [Illumina TruPath Genome WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-trupath-genome-wgs.md) - [Illumina scRNA](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-scrna.md) - [Illumina scRNA Perturb seq](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/illumina-scrna-perturb-seq.md) - [Other scRNA prep](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/other-scrna-prep.md) - [RNA Amplicon](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-amplicon.md) - [RNA Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-panel.md) - [RNA WTS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/rna-wts.md) - [5 Base DNA Germline Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-panel.md) - [5 Base DNA Germline Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-panel-umi.md) - [5 Base DNA Germline WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-germline-wgs.md) - [5 Base DNA Somatic Tumor-Normal Solid Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-panel.md) - [5 Base DNA Somatic Tumor-Normal Solid WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only Solid Panel](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel.md) - [5 Base DNA Somatic Tumor-Only Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel-umi.md) - [5 Base DNA Somatic Tumor-Only Solid WGS](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md) - [DRAGEN WGS Germline Accuracy](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline.md) - [Small Variants](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/small_variants_accuracy.md) - [Copy Number Variation](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/copy_number_variation_accuracy.md) - [Structural Variants](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/structural_variants_accuracy.md) - [HLA Genotyping](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/hla_genotyping_accuracy.md) - [Targeted Callers](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/targeted_callers_accuracy.md) - [Multi-Region Joint Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/mrjd_accuracy.md) - [Ploidy Estimator](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/ploidy_estimator_accuracy.md) - [Tandem Repeats](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/tandem_repeats_accuracy.md) - [DRAGEN Reference Support](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-reference-support.md) - [Prepare a Reference Genome](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-reference-support/prepare-a-reference-genome.md) - [DRAGEN DNA Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline.md) - [DNA Mapping](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/dna-map-align.md) - [Read Trimming](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/read-trimming.md) - [Sorting and Duplicate Marking](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sort-dupmark.md) - [Small Variant Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling.md) - [ROH Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/roh-caller.md) - [B-Allele Frequency Output](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/baf-output.md) - [Somatic Mode](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) - [Somatic ML for Small VC (Beta)](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/somatic-mode/somatic-ml.md) - [Pedigree Analysis](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/pedigree-analysis.md) - [De Novo Small Variant Filtering](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/filtering.md) - [Autogenerated MD5SUM for VCF Files](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) - [Force Genotyping](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) - [Machine Learning for Variant Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) - [Evidence BAM](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) - [Mosaic Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) - [VCF Imputation](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) - [Multi-Region Joint Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) - [Small Variant Calling Metrics](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/small-variant-calling-metrics.md) - [Copy Number Variant Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview.md) - [Germline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline.md) - [Germline Depth-Only](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline/cnv-germline-legacy.md) - [Somatic](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-somatic.md) - [Reference](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-reference.md) - [Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/repeat-expansions.md) - [De Novo Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) - [Targeted Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller.md) - [CYP2B6 Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) - [CYP2D6 Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) - [CYP21A2 Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) - [GBA Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/gba-calling.md) - [HBA Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/hba-calling.md) - [LPA Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/lpa-calling.md) - [Rh Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/rh-calling.md) - [SMN Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/targeted-caller/smn-calling.md) - [Structural Variant Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling.md) - [Structural Variant De Novo Quality Scoring](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) - [Structural Variant IGV Tutorial](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling/sv-igv-tutorial.md) - [Population Genotyping](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/iterative-gvcf-genotyper.md) - [Filter Duplicate Variants](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/variant-deduplication.md) - [Ploidy Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling.md) - [Ploidy Estimator](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) - [Ploidy Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) - [Multi Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/multi-caller.md) - [HLA Typing](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/hla-typing.md) - [Biomarkers](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers.md) - [Tumor Mutational Burden](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) - [Microsatellite Instability](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-msi.md) - [Homologous Recombination Deficiency](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) - [Mutational Signatures](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-mutational-signatures.md) - [BRCA Large Genomic Rearrangement](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) - [DRAGEN Fragmentomics](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) - [Downsampling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/downsampling.md) - [Fractional (Raw Reads) Downsampling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/downsampling/fractional-downsampler.md) - [Unique Molecular Identifiers](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/unique-molecular-identifiers.md) - [Indel Re-aligner (Beta)](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/indel-realigner.md) - [Star Allele Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/star-allele-caller.md) - [High Coverage Analysis](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/high-coverage.md) - [Population Haplotyping](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/population-haplotyping.md) - [DUX4 Rearrangement Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/dux4-rearrangement-caller.md) - [Oncovirus Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/oncovirus-detection.md) - [DRAGEN RNA Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline.md) - [RNA Alignment](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/rna-alignment.md) - [Gene Fusion Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/gene-fusion-detection.md) - [Gene Expression Quantification](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/gene-expression-quantification.md) - [RNA Variant Calling](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/rna-variant-calling.md) - [Splice Variant Caller](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-rna-pipeline/splice-variant-caller.md) - [DRAGEN Single Cell Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline.md) - [Illumina PIPseq scRNA](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-illumina.md) - [Other scRNA Prep](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scrna-other.md) - [scATAC](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-scatac.md) - [Single-Cell Multiomics](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-single-cell-pipeline/dragen-multiomics.md) - [Illumina TruPath Genome Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-trupath-pipeline.md) - [DRAGEN Methylation Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-methylation-pipeline.md) - [Bisulfite and TAPS Methylation Prep](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-methylation-pipeline/dragen-methylation-pipeline.md) - [DRAGEN 5-Base Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-5-base.md) - [Illumina 5-base Prep](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-5-base/dragen-5base-pipeline.md) - [DRAGEN MRD Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/mrd.md) - [DRAGEN Amplicon Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-amplicon-pipeline.md) - [DRAGEN 16S Pipeline](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline.md) - [16S Pipeline Pre-Built Database](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/dragen-16s-db.md) - [16S Custom Database](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/dragen-16s-custom-db.md) - [16S Sample JSON](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-16s-pipeline/report-json-format.md) - [DRAGEN K-mer Classifier](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier.md) - [Prebuilt K-mer Databases](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/prebuilt-kmer-dbs.md) - [K-mer Classifier Database Builder](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/kmer-class-db-builder.md) - [Microbial Binner Database](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/kmer-classifier/microbial-binner.md) - [DRAGEN Microbial Enrichment Plus](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview.md) - [Reference Databases](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-databases.md) - [Custom Database](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-custom-database.md) - [Output](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dme-plus-overview/dme-plus-output.md) - [BCL conversion](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/bcl-conversion.md) - [DRAGEN QC Metrics](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting.md) - [Minimal Checklist](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/minimal_checklist.md) - [Contamination Detection](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/contamination-detection.md) - [FastQC](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/dragen-fastqc.md) - [CheckFingerprint](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/checkfingerprint.md) - [JSON Metrics Reporting](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/qc-metrics-reporting/json-metrics-reporting.md) - [Illumina Connected Annotations](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/nirvana.md) - [ORA Compression](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/ora-compression.md) - [Command Line Options](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/command-line-options.md) - [Docker Requirements](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/command-line-options/docker-requirements.md) - [DRAGEN Reports](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-reports.md) - [Tools and Utilities](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/tools-and-utilities.md) - [DRAGEN Server](https://help.dragen.illumina.com/dragen-v4.5/reference/platform-maintenance.md) - [DRAGEN Multi-Cloud](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud.md) - [DRAGEN on AWS](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-aws.md) - [DRAGEN on AWS Batch](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-aws-batch.md) - [DRAGEN on Microsoft Azure](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-azure.md) - [Run DRAGEN VM on Azure](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) - [DRAGEN on Microsoft Azure Batch](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/azure-batch.md) - [Azure Batch Run Modes](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) - [DRAGEN Pricing and Licensing](https://help.dragen.illumina.com/dragen-v4.5/reference/licensing.md) - [DRAGEN OnPrem Server Licensing](https://help.dragen.illumina.com/dragen-v4.5/reference/licensing/onprem_licensing.md) - [DRAGEN Cloud FPGA BYOL](https://help.dragen.illumina.com/dragen-v4.5/reference/licensing/cloud_licensing.md) - [Support](https://help.dragen.illumina.com/dragen-v4.5/reference/technical-assistance.md) - [Resource Files](https://help.dragen.illumina.com/dragen-v4.5/reference/resource-files.md) - [Noise Baselines](https://help.dragen.illumina.com/dragen-v4.5/reference/resource-files/prebuilt-baseline-files.md) - [Supplementary Information](https://help.dragen.illumina.com/dragen-v4.5/reference/additional-resources.md) - [DRAGEN Product Obsolescence Notices](https://help.dragen.illumina.com/dragen-v4.5/reference/eol-transition.md) - [F2 Validation](https://help.dragen.illumina.com/dragen-v4.5/reference/f2-validation.md) - [Troubleshooting](https://help.dragen.illumina.com/dragen-v4.5/reference/troubleshooting.md) - [Citing DRAGEN software](https://help.dragen.illumina.com/dragen-v4.5/reference/citing-dragen.md) - [DRAGEN Publications](https://help.dragen.illumina.com/dragen-v4.5/reference/dragen-publications.md) - [Release Notes](https://help.dragen.illumina.com/dragen-v4.5/reference/release-notes-readme.md) - [DRAGEN v4.5.4 Release Notes](https://help.dragen.illumina.com/dragen-v4.5/reference/release-notes-readme/dragen-crn-v4.5.4.md) - [Revision History](https://help.dragen.illumina.com/dragen-v4.5/reference/revision-history.md) ## DRAGEN v4.4 - [Illumina® DRAGEN™ Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.4/overview/welcome-page.md) - [DRAGEN Applications](https://help.dragen.illumina.com/dragen-v4.4/overview/key-applications.md) - [Deployment Options](https://help.dragen.illumina.com/dragen-v4.4/overview/deployment-options.md) - [DRAGEN v4.4](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4.md) - [Getting Started](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/getting-started.md) - [DRAGEN Host Software](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software.md) - [DRAGEN Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software/dragen-platform.md) - [Clinical Research Workflows](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps.md) - [Common Product Features](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common.md) - [Sample Sheets](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/sample-sheet-introduction.md) - [Run Planning](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning.md) - [Sample Sheet Creation in BaseSpace](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/basespace-run-planning-tool.md) - [Custom Config Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/custom_config.md) - [DRAGEN Server App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server.md) - [Advanced Topics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced.md) - [Data Management](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/data-storage.md) - [Illumina Connected Insights Local](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/ici-on-prem.md) - [ICA Cloud App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud.md) - [Variant Interpretation with Illumina Connected Insights](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud/ici-setup.md) - [DRAGEN Heme WGS Tumor Only Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline.md) - [Quick Start](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation.md) - [Launching Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced.md) - [Custom Config Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup.md) - [Launching Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md) - [ICA Specific Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis/output.md) - [Advanced Topics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced.md) - [Custom Workflow](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/workflow.md) - [Custom Config Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md) - [Post Processing](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/post-processing.md) - [Analysis Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-output.md) - [Analysis Methods](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-methods.md) - [Troubleshooting](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/troubleshooting.md) - [DRAGEN Solid WGS Tumor Normal Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline.md) - [Quick Start](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start.md) - [Sample Sheet Requirements](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements/sample-sheet-templates.md) - [DRAGEN Server App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation.md) - [Launching Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis.md) - [Command Line Options](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/command-line-options.md) - [Local Specific Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced.md) - [Custom Config Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup.md) - [Launching Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/launching-analysis.md) - [Advanced Topics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced.md) - [Custom Workflow](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced/workflow.md) - [Analysis Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-output.md) - [Analysis Methods](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-methods.md) - [Troubleshooting](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/troubleshooting.md) - [DRAGEN Recipes](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes.md) - [DNA Germline Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel-umi.md) - [DNA Germline Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel.md) - [DNA Germline WES UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes-umi.md) - [DNA Germline WES](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes.md) - [DNA Germline WGS UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs-umi.md) - [DNA Germline WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs.md) - [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) - [DNA Somatic Tumor-Normal Solid Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) - [DNA Somatic Tumor-Normal Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) - [DNA Somatic Tumor-Normal Solid WES](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) - [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) - [DNA Somatic Tumor-Normal Solid WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) - [DNA Somatic Tumor-Only Heme WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) - [DNA Somatic Tumor-Only Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) - [DNA Somatic Tumor-Only Solid Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) - [DNA Somatic Tumor-Only Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) - [DNA Somatic Tumor-Only Solid WES](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) - [DNA Somatic Tumor-Only Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) - [DNA Somatic Tumor-Only Solid WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) - [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) - [Illumina scRNA](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/illumina-scrna.md) - [Other scRNA prep](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/other-scrna-prep.md) - [RNA Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-panel.md) - [RNA WTS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-wts.md) - [DNA Amplicon](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-amplicon.md) - [RNA Amplicon](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-amplicon.md) - [5 Base DNA Germline Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel-umi.md) - [5 Base DNA Germline Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel.md) - [5 Base DNA Germline WGS UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs-umi.md) - [5 Base DNA Germline WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs.md) - [5 Base DNA Somatic Tumor-Normal Solid Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-panel.md) - [5 Base DNA Somatic Tumor-Normal Solid WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel-umi.md) - [5 Base DNA Somatic Tumor-Only Solid Panel](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel.md) - [5 Base DNA Somatic Tumor-Only Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs-umi.md) - [5 Base DNA Somatic Tumor-Only Solid WGS](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs.md) - [5 Base DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md) - [DRAGEN Reference Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support.md) - [Prepare a Reference Genome](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support/prepare-a-reference-genome.md) - [DRAGEN DNA Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline.md) - [DNA Mapping](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dna-map-align.md) - [Read Trimming](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/read-trimming.md) - [DRAGEN FASTQC](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dragen-fastqc.md) - [Sorting and Duplicate Marking](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sort-dupmark.md) - [Small Variant Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling.md) - [ROH Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/roh-caller.md) - [B-Allele Frequency Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/baf-output.md) - [Somatic Mode](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) - [Pedigree Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/pedigree-analysis.md) - [De Novo Small Variant Filtering](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/filtering.md) - [Autogenerated MD5SUM for VCF Files](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) - [Force Genotyping](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) - [Machine Learning for Variant Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) - [Evidence BAM](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) - [Mosaic Detection](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) - [VCF Imputation](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) - [Multi-Region Joint Detection](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) - [Copy Number Variant Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling.md) - [Available pipelines](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines.md) - [Germline CNV Calling (WGS/WES)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/germline-cnv-calling.md) - [Germline CNV Calling ASCN (WGS)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/germline-cnv-calling-wgs-ascn.md) - [Multisample Germline CNV Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/multisample-cnv-calling.md) - [Somatic CNV Calling ASCN (WGS)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wgs.md) - [Somatic CNV Calling WES](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wes.md) - [Somatic CNV Calling ASCN (WES)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wes-ascn.md) - [Additional documentation](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation.md) - [CNV Input](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-input.md) - [CNV Preprocessing](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-preprocessing.md) - [CNV Segmentation](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-segmentation.md) - [CNV Output](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-output.md) - [CNV ASCN module](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-ascn.md) - [CNV with SV Support](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-with-sv-support.md) - [Cytogenetics Modality](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cytogenetics-modality.md) - [Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions.md) - [De Novo Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) - [Targeted Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller.md) - [CYP2B6 Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) - [CYP2D6 Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) - [CYP21A2 Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) - [GBA Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/gba-calling.md) - [HBA Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/hba-calling.md) - [LPA Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/lpa-calling.md) - [Rh Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/rh-calling.md) - [SMN Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/smn-calling.md) - [Structural Variant Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling.md) - [Structural Variant De Novo Quality Scoring](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) - [Structural Variant IGV Tutorial](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-igv-tutorial.md) - [VNTR Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/vntr-calling.md) - [Population Genotyping](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/iterative-gvcf-genotyper.md) - [Filter Duplicate Variants](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/variant-deduplication.md) - [Ploidy Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling.md) - [Ploidy Estimator](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) - [Ploidy Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) - [Multi Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/multi-caller.md) - [QC Metrics Reporting](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/qc-metrics-reporting.md) - [JSON Metrics Reporting](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/json-metrics-reporting.md) - [HLA Typing](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/hla-typing.md) - [Biomarkers](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers.md) - [Tumor Mutational Burden](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) - [Microsatellite Instability](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-msi.md) - [Homologous Recombination Deficiency](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) - [BRCA Large Genomic Rearrangment](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) - [DRAGEN Fragmentomics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) - [Downsampling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling.md) - [Fractional (Raw Reads) Downsampling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling/fractional-downsampler.md) - [Unique Molecular Identifiers](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers.md) - [Indel Re-aligner (Beta)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/indel-realigner.md) - [Star Allele Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/star-allele-caller.md) - [High Coverage Analysis](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/high-coverage.md) - [CheckFingerprint](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/checkfingerprint.md) - [Population Haplotyping (Beta)](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/population-haplotyping.md) - [DUX4 Rearrangement Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dux4-rearrangement-caller.md) - [DRAGEN RNA Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline.md) - [RNA Alignment](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-alignment.md) - [Gene Fusion Detection](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-fusion-detection.md) - [Gene Expression Quantification](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-expression-quantification.md) - [RNA Variant Calling](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-variant-calling.md) - [Splice Variant Caller](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/splice-variant-caller.md) - [DRAGEN Single Cell Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline.md) - [Illumina PIPseq scRNA](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna-pipseq.md) - [Other scRNA Prep](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna.md) - [scATAC](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scatac.md) - [Single-Cell Multiomics](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-multiomics.md) - [DRAGEN Methylation Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline.md) - [Illumina 5-base Prep](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline.md) - [Other Methylation Prep](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-methylation-pipeline.md) - [DRAGEN MRD Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/mrd.md) - [DRAGEN Amplicon Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-amplicon-pipeline.md) - [DRAGEN 16S Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline.md) - [16S Pipeline Pre-Built Database](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-db.md) - [16S Custom Database](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-custom-db.md) - [16S Sample JSON](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/report-json-format.md) - [Explify Analysis Pipeline](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/pipeline.md) - [Kmer Classifier](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-classifier.md) - [Kmer Classifier Database Builder](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-class-db-builder.md) - [BCL conversion](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/bcl-conversion.md) - [Illumina Connected Annotations](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/nirvana.md) - [ORA Compression](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/ora-compression.md) - [Command Line Options](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/command-line-options.md) - [Docker Requirements](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/command-line-options/docker-requirements.md) - [DRAGEN Reports](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-reports.md) - [Tools and Utilities](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/tools-and-utilities.md) - [DRAGEN Server](https://help.dragen.illumina.com/dragen-v4.4/reference/platform-maintenance.md) - [DRAGEN Application Manager](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-application-manager.md) - [DRAGEN Multi-Cloud](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud.md) - [DRAGEN on AWS](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-aws.md) - [DRAGEN on AWS Batch](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-aws-batch.md) - [DRAGEN on Microsoft Azure](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-azure.md) - [Run DRAGEN VM on Azure](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) - [DRAGEN on Microsoft Azure Batch](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/azure-batch.md) - [Azure Batch Run Modes](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) - [DRAGEN Licensing](https://help.dragen.illumina.com/dragen-v4.4/reference/licensing.md) - [DRAGEN Server Licensing](https://help.dragen.illumina.com/dragen-v4.4/reference/licensing/onprem_licensing.md) - [DRAGEN Cloud Licensing](https://help.dragen.illumina.com/dragen-v4.4/reference/licensing/cloud_licensing.md) - [Support](https://help.dragen.illumina.com/dragen-v4.4/reference/technical-assistance.md) - [Resource Files](https://help.dragen.illumina.com/dragen-v4.4/reference/resource-files.md) - [Noise Baselines](https://help.dragen.illumina.com/dragen-v4.4/reference/resource-files/prebuilt-baseline-files.md) - [Supplementary Information](https://help.dragen.illumina.com/dragen-v4.4/reference/additional-resources.md) - [DRAGEN Product Obsolescence Notices](https://help.dragen.illumina.com/dragen-v4.4/reference/eol-transition.md) - [F2 Validation](https://help.dragen.illumina.com/dragen-v4.4/reference/f2-validation.md) - [Troubleshooting](https://help.dragen.illumina.com/dragen-v4.4/reference/troubleshooting.md) - [Citing DRAGEN software](https://help.dragen.illumina.com/dragen-v4.4/reference/citing-dragen.md) - [DRAGEN Publications](https://help.dragen.illumina.com/dragen-v4.4/reference/dragen-publications.md) - [Release Notes](https://help.dragen.illumina.com/dragen-v4.4/reference/release-notes-readme.md) - [Revision History](https://help.dragen.illumina.com/dragen-v4.4/reference/revision-history.md) ## DRAGEN v4.3 - [Illumina® DRAGEN™ Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.3/overview/welcome-page.md) - [DRAGEN Applications](https://help.dragen.illumina.com/dragen-v4.3/overview/key-applications.md) - [Deployment Options](https://help.dragen.illumina.com/dragen-v4.3/overview/deployment-options.md) - [DRAGEN v4.3](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3.md) - [Getting Started](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/getting-started.md) - [DRAGEN Host Software](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-host-software.md) - [DRAGEN Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-host-software/dragen-platform.md) - [DRAGEN Reference Support](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-reference-support.md) - [Prepare a Reference Genome](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-reference-support/prepare-a-reference-genome.md) - [DRAGEN DNA Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline.md) - [DNA Mapping](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dna-map-align.md) - [Read Trimming](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/read-trimming.md) - [DRAGEN FASTQC](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dragen-fastqc.md) - [Sorting and Duplicate Marking](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sort-dupmark.md) - [Small Variant Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling.md) - [ROH Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/roh-caller.md) - [B-Allele Frequency Output](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/baf-output.md) - [Somatic Mode](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) - [Joint Analysis](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/joint-analysis.md) - [De Novo Small Variant Filtering](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/filtering.md) - [Autogenerated MD5SUM for VCF Files](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) - [Force Genotyping](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) - [Machine Learning for Variant Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) - [Evidence BAM](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) - [Mosaic Detection](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) - [VCF Imputation](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) - [Multi-Region Joint Detection](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) - [Copy Number Variant Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling.md) - [CNV Output](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/cnv-output.md) - [CNV with SV Support](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/cnv-with-sv-support.md) - [Multisample CNV Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/multisample-cnv-calling.md) - [Somatic CNV Calling WGS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wgs.md) - [Somatic CNV Calling WES](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wes.md) - [Allele Specific CNV for Somatic WES CNV](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/cnv-calling/somatic-cnv-calling-wes-ascn.md) - [Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/repeat-expansions.md) - [De Novo Repeat Expansion Detection](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) - [Targeted Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller.md) - [CYPDB6 Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) - [CYP2D6 Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) - [CYP21A2 Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) - [GBA Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/gba-calling.md) - [HBA Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/hba-calling.md) - [LPA Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/lpa-calling.md) - [Rh Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/rh-calling.md) - [SMN Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller/smn-calling.md) - [Structural Variant Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sv-calling.md) - [Structural Variant De Novo Quality Scoring](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) - [VNTR Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/vntr-calling.md) - [Filter Duplicate Variants](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/variant-deduplication.md) - [Ploidy Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling.md) - [Ploidy Estimator](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) - [Ploidy Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) - [Multi Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/multi-caller.md) - [QC Metrics Reporting](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/qc-metrics-reporting.md) - [HLA Typing](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/hla-typing.md) - [Biomarkers](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers.md) - [Tumor Mutational Burden](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) - [Microsatellite Instability](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-msi.md) - [Homologous Recombination Deficiency](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) - [BRCA Large Genomic Rearrangment](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) - [DRAGEN Fragmentomics](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) - [Downsampling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling.md) - [Fractional (Raw Reads) Downsampling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling/fractional-downsampler.md) - [Effective Coverage Downsampling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/downsampling/downsampling.md) - [Unique Molecular Identifiers](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/unique-molecular-identifiers.md) - [Indel Re-aligner (Beta)](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/indel-realigner.md) - [Star Allele Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/star-allele-caller.md) - [High Coverage Analysis](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/high-coverage.md) - [CheckFingerprint](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/checkfingerprint.md) - [Population Haplotyping (Beta)](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/population-haplotyping.md) - [DUX4 Rearrangement Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/dux4-rearrangement-caller.md) - [DRAGEN RNA Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline.md) - [RNA Alignment](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/rna-alignment.md) - [Gene Fusion Detection](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/gene-fusion-detection.md) - [Gene Expression Quantification](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/gene-expression-quantification.md) - [RNA Variant Calling](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/rna-variant-calling.md) - [Splice Variant Caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-rna-pipeline/splice-variant-caller.md) - [DRAGEN Single-Cell Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline.md) - [scRNA](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-scrna.md) - [scATAC](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-scatac.md) - [Single-Cell Multiomics](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-single-cell-pipeline/dragen-multiomics.md) - [DRAGEN Methylation Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-methylation-pipeline.md) - [DRAGEN Amplicon Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-amplicon-pipeline.md) - [Explify Analysis Pipeline](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/pipeline.md) - [Kmer Classifier](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/pipeline/kmer-classifier.md) - [Kmer Classifier Database Builder](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/pipeline/kmer-class-db-builder.md) - [DRAGEN Recipes](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes.md) - [DNA Germline Panel UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-panel-umi.md) - [DNA Germline Panel](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-panel.md) - [DNA Germline WES UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wes-umi.md) - [DNA Germline WES](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wes.md) - [DNA Germline WGS UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wgs-umi.md) - [DNA Germline WGS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-germline-wgs.md) - [DNA Somatic Tumor-Normal Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) - [DNA Somatic Tumor-Normal Solid Panel](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) - [DNA Somatic Tumor-Normal Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) - [DNA Somatic Tumor-Normal Solid WES](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) - [DNA Somatic Tumor-Normal Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) - [DNA Somatic Tumor-Normal Solid WGS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) - [DNA Somatic Tumor-Only Heme WGS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) - [DNA Somatic Tumor-Only Solid Panel UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) - [DNA Somatic Tumor-Only Solid Panel](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) - [DNA Somatic Tumor-Only Solid WES UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) - [DNA Somatic Tumor-Only Solid WES](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) - [DNA Somatic Tumor-Only Solid WGS UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) - [DNA Somatic Tumor-Only Solid WGS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) - [DNA Somatic Tumor-Only ctDNA Panel UMI](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) - [RNA Panel](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/rna-panel.md) - [RNA WTS](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-recipes/rna-wts.md) - [BCL conversion](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/bcl-conversion.md) - [Illumina Connected Annotations](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/nirvana.md) - [ORA Compression](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/ora-compression.md) - [Command Line Options](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/command-line-options.md) - [DRAGEN Reports](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-reports.md) - [Tools and Utilities](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/tools-and-utilities.md) - [DRAGEN Server](https://help.dragen.illumina.com/dragen-v4.3/reference/platform-maintenance.md) - [DRAGEN Multi-Cloud](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud.md) - [DRAGEN on AWS](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-aws.md) - [DRAGEN on AWS Batch](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-aws-batch.md) - [DRAGEN on Microsoft Azure](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-azure.md) - [Run DRAGEN VM on Azure](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/dragen-on-azure/run-vm-on-azure.md) - [DRAGEN on Microsoft Azure Batch](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/azure-batch.md) - [Azure Batch Run Modes](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-multi-cloud/azure-batch/run-azure-modes.md) - [DRAGEN Licensing](https://help.dragen.illumina.com/dragen-v4.3/reference/licensing.md) - [DRAGEN Server Licensing](https://help.dragen.illumina.com/dragen-v4.3/reference/licensing/onprem_licensing.md) - [DRAGEN Cloud Licensing](https://help.dragen.illumina.com/dragen-v4.3/reference/licensing/cloud_licensing.md) - [Support](https://help.dragen.illumina.com/dragen-v4.3/reference/technical-assistance.md) - [Resource Files](https://help.dragen.illumina.com/dragen-v4.3/reference/resource-files.md) - [Noise Baselines](https://help.dragen.illumina.com/dragen-v4.3/reference/resource-files/prebuilt-baseline-files.md) - [Supplementary Information](https://help.dragen.illumina.com/dragen-v4.3/reference/additional-resources.md) - [DRAGEN Product Obsolescence Notices](https://help.dragen.illumina.com/dragen-v4.3/reference/eol-transition.md) - [F2 Validation](https://help.dragen.illumina.com/dragen-v4.3/reference/f2-validation.md) - [Troubleshooting](https://help.dragen.illumina.com/dragen-v4.3/reference/troubleshooting.md) - [Citing DRAGEN software](https://help.dragen.illumina.com/dragen-v4.3/reference/citing-dragen.md) - [DRAGEN Publications](https://help.dragen.illumina.com/dragen-v4.3/reference/dragen-publications.md) - [Release Notes](https://help.dragen.illumina.com/dragen-v4.3/reference/release-notes-readme.md) - [Revision History](https://help.dragen.illumina.com/dragen-v4.3/reference/revision-history.md) ## DRAGEN 4.5 (Illumina TruPath Genome) - [Illumina® DRAGEN™ Secondary Analysis](https://help.dragen.illumina.com/dragen-v4.5-trupath/overview/welcome-page.md) - [DRAGEN v4.5](https://help.dragen.illumina.com/dragen-v4.5-trupath/product-guides/dragen-v4.5.md) - [Illumina TruPath Genome Prep](https://help.dragen.illumina.com/dragen-v4.5-trupath/product-guides/dragen-v4.5/dragen-trupath-pipeline.md) - [Illumina TruPath Genome WGS Recipe](https://help.dragen.illumina.com/dragen-v4.5-trupath/product-guides/dragen-v4.5/illumina-trupath-genome-wgs.md) --- # Agent Instructions This documentation is published with GitBook. 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