# DRAGEN v4.4 - [Getting Started](/dragen-v4.4/product-guide/dragen-v4.4/getting-started.md) - [DRAGEN Host Software](/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software.md) - [DRAGEN Secondary Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-host-software/dragen-platform.md) - [Clinical Research Workflows](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps.md) - [Common Product Features](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common.md) - [Sample Sheets](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/sample-sheet-introduction.md) - [Run Planning](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning.md) - [Sample Sheet Creation in BaseSpace](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/basespace-run-planning-tool.md) - [Custom Config Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/run-planning/custom_config.md) - [DRAGEN Server App](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server.md) - [Advanced Topics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced.md) - [Data Management](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/data-storage.md) - [Illumina Connected Insights Local](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/server/advanced/ici-on-prem.md) - [ICA Cloud App](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud.md) - [Variant Interpretation with Illumina Connected Insights](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/common/cloud/ici-setup.md) - [DRAGEN Heme WGS Tumor Only Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline.md) - [Quick Start](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start.md) - [Sample Sheet Requirements](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation.md) - [Launching Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis.md) - [Command Line Options](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced.md) - [Custom Config Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup.md) - [Launching Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis.md) - [ICA Specific Output](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/launching-analysis/output.md) - [Advanced Topics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced.md) - [Custom Workflow](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/workflow.md) - [Custom Config Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md) - [Post Processing](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/setup/advanced/post-processing.md) - [Analysis Output](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-output.md) - [Analysis Methods](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/analysis-methods.md) - [Troubleshooting](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/troubleshooting.md) - [DRAGEN Solid WGS Tumor Normal Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline.md) - [Quick Start](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start.md) - [Sample Sheet Requirements](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/quick-start/sample-sheet-requirements.md) - [Templates](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation.md) - [Launching Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis.md) - [Command Line Options](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/launching-analysis/output.md) - [Advanced Topics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced.md) - [Custom Config Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/installation/advanced/custom_config.md) - [ICA Cloud App](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup.md) - [Launching Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/launching-analysis.md) - [Advanced Topics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced.md) - [Custom Workflow](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/setup/advanced/workflow.md) - [Analysis Output](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-output.md) - [Analysis Methods](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/analysis-methods.md) - [Troubleshooting](/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-solid-wgs-tn-pipeline/troubleshooting.md) - [DRAGEN Recipes](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes.md) - [DNA Germline Panel UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel-umi.md) - [DNA Germline Panel](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-panel.md) - [DNA Germline WES UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes-umi.md) - [DNA Germline WES](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wes.md) - [DNA Germline WGS UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs-umi.md) - [DNA Germline WGS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-germline-wgs.md) - [DNA Somatic Tumor-Normal Solid Panel UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md) - [DNA Somatic Tumor-Normal Solid Panel](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md) - [DNA Somatic Tumor-Normal Solid WES UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md) - [DNA Somatic Tumor-Normal Solid WES](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md) - [DNA Somatic Tumor-Normal Solid WGS UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md) - [DNA Somatic Tumor-Normal Solid WGS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md) - [DNA Somatic Tumor-Only Heme WGS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md) - [DNA Somatic Tumor-Only Solid Panel UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md) - [DNA Somatic Tumor-Only Solid Panel](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-panel.md) - [DNA Somatic Tumor-Only Solid WES UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md) - [DNA Somatic Tumor-Only Solid WES](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wes.md) - [DNA Somatic Tumor-Only Solid WGS UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md) - [DNA Somatic Tumor-Only Solid WGS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md) - [DNA Somatic Tumor-Only ctDNA Panel UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md) - [Illumina scRNA](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/illumina-scrna.md) - [Other scRNA prep](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/other-scrna-prep.md) - [RNA Panel](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-panel.md) - [RNA WTS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-wts.md) - [DNA Amplicon](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/dna-amplicon.md) - [RNA Amplicon](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/rna-amplicon.md) - [5 Base DNA Germline Panel UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel-umi.md) - [5 Base DNA Germline Panel](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-panel.md) - [5 Base DNA Germline WGS UMI](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs-umi.md) - [5 Base DNA Germline WGS](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-germline-wgs.md) - [5 Base DNA Somatic Tumor-Normal Solid Panel](/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](/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](/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](/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](/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](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md) - [DRAGEN Reference Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support.md) - [Prepare a Reference Genome](/dragen-v4.4/product-guide/dragen-v4.4/dragen-reference-support/prepare-a-reference-genome.md) - [DRAGEN DNA Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline.md) - [DNA Mapping](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dna-map-align.md) - [Read Trimming](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/read-trimming.md) - [DRAGEN FASTQC](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dragen-fastqc.md) - [Sorting and Duplicate Marking](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sort-dupmark.md) - [Small Variant Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling.md) - [ROH Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/roh-caller.md) - [B-Allele Frequency Output](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/baf-output.md) - [Somatic Mode](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) - [Pedigree Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/pedigree-analysis.md) - [De Novo Small Variant Filtering](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/filtering.md) - [Autogenerated MD5SUM for VCF Files](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/small-variant-calling2.md) - [Force Genotyping](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/force-genotyping.md) - [Machine Learning for Variant Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/ml-for-vc.md) - [Evidence BAM](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/evidence-bam.md) - [Mosaic Detection](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/mosaic-detection.md) - [VCF Imputation](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/vcf-imputation.md) - [Multi-Region Joint Detection](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md) - [Copy Number Variant Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling.md) - [Available pipelines](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines.md) - [Germline CNV Calling (WGS/WES)](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/germline-cnv-calling.md) - [Germline CNV Calling ASCN (WGS)](/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](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/multisample-cnv-calling.md) - [Somatic CNV Calling ASCN (WGS)](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wgs.md) - [Somatic CNV Calling WES](/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)](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/available-pipelines/somatic-cnv-calling-wes-ascn.md) - [Additional documentation](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation.md) - [CNV Input](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-input.md) - [CNV Preprocessing](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-preprocessing.md) - [CNV Segmentation](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-segmentation.md) - [CNV Output](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-output.md) - [CNV ASCN module](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-ascn.md) - [CNV with SV Support](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-with-sv-support.md) - [Cytogenetics Modality](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cytogenetics-modality.md) - [Repeat Expansion Detection](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions.md) - [De Novo Repeat Expansion Detection](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/repeat-expansions/de-novo-str-detection.md) - [Targeted Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller.md) - [CYP2B6 Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2b6-calling.md) - [CYP2D6 Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp2d6-calling.md) - [CYP21A2 Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/cyp21a2-calling.md) - [GBA Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/gba-calling.md) - [HBA Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/hba-calling.md) - [LPA Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/lpa-calling.md) - [Rh Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/rh-calling.md) - [SMN Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/targeted-caller/smn-calling.md) - [Structural Variant Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling.md) - [Structural Variant De Novo Quality Scoring](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-denovo-quality-scoring.md) - [Structural Variant IGV Tutorial](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling/sv-igv-tutorial.md) - [VNTR Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/vntr-calling.md) - [Population Genotyping](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/iterative-gvcf-genotyper.md) - [Filter Duplicate Variants](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/variant-deduplication.md) - [Ploidy Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling.md) - [Ploidy Estimator](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-estimator.md) - [Ploidy Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/ploidy-caller.md) - [Multi Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/multi-caller.md) - [QC Metrics Reporting](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/qc-metrics-reporting.md) - [JSON Metrics Reporting](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/json-metrics-reporting.md) - [HLA Typing](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/hla-typing.md) - [Biomarkers](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers.md) - [Tumor Mutational Burden](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) - [Microsatellite Instability](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-msi.md) - [Homologous Recombination Deficiency](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) - [BRCA Large Genomic Rearrangment](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md) - [DRAGEN Fragmentomics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-fragmentomics.md) - [Downsampling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling.md) - [Fractional (Raw Reads) Downsampling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/downsampling/fractional-downsampler.md) - [Unique Molecular Identifiers](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/unique-molecular-identifiers.md) - [Indel Re-aligner (Beta)](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/indel-realigner.md) - [Star Allele Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/star-allele-caller.md) - [High Coverage Analysis](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/high-coverage.md) - [CheckFingerprint](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/checkfingerprint.md) - [Population Haplotyping (Beta)](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/population-haplotyping.md) - [DUX4 Rearrangement Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-dna-pipeline/dux4-rearrangement-caller.md) - [DRAGEN RNA Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline.md) - [RNA Alignment](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-alignment.md) - [Gene Fusion Detection](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-fusion-detection.md) - [Gene Expression Quantification](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/gene-expression-quantification.md) - [RNA Variant Calling](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/rna-variant-calling.md) - [Splice Variant Caller](/dragen-v4.4/product-guide/dragen-v4.4/dragen-rna-pipeline/splice-variant-caller.md) - [DRAGEN Single Cell Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline.md) - [Illumina PIPseq scRNA](/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna-pipseq.md) - [Other scRNA Prep](/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scrna.md) - [scATAC](/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-scatac.md) - [Single-Cell Multiomics](/dragen-v4.4/product-guide/dragen-v4.4/dragen-single-cell-pipeline/dragen-multiomics.md) - [DRAGEN Methylation Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline.md) - [Illumina 5-base Prep](/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline.md) - [Other Methylation Prep](/dragen-v4.4/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-methylation-pipeline.md) - [DRAGEN MRD Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/mrd.md) - [DRAGEN Amplicon Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-amplicon-pipeline.md) - [DRAGEN 16S Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline.md) - [16S Pipeline Pre-Built Database](/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-db.md) - [16S Custom Database](/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/dragen-16s-custom-db.md) - [16S Sample JSON](/dragen-v4.4/product-guide/dragen-v4.4/dragen-16s-pipeline/report-json-format.md) - [Explify Analysis Pipeline](/dragen-v4.4/product-guide/dragen-v4.4/pipeline.md) - [Kmer Classifier](/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-classifier.md) - [Kmer Classifier Database Builder](/dragen-v4.4/product-guide/dragen-v4.4/pipeline/kmer-class-db-builder.md) - [BCL conversion](/dragen-v4.4/product-guide/dragen-v4.4/bcl-conversion.md) - [Illumina Connected Annotations](/dragen-v4.4/product-guide/dragen-v4.4/nirvana.md) - [ORA Compression](/dragen-v4.4/product-guide/dragen-v4.4/ora-compression.md) - [Command Line Options](/dragen-v4.4/product-guide/dragen-v4.4/command-line-options.md) - [Docker Requirements](/dragen-v4.4/product-guide/dragen-v4.4/command-line-options/docker-requirements.md) - [DRAGEN Reports](/dragen-v4.4/product-guide/dragen-v4.4/dragen-reports.md) - [Tools and Utilities](/dragen-v4.4/product-guide/dragen-v4.4/tools-and-utilities.md)