> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes.md).

# DRAGEN Recipes

### Overview

The following sub-pages contain recommended command line options for specific DRAGEN pipelines. For an overview of DRAGEN command line parsing, also see [Multicaller Workflows](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/multi-caller.md)

#### Germline Pipelines

* [DNA Germline Amplicon](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-amplicon.md)
* [DNA Germline Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-panel.md)
* [DNA Germline WES](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-wes.md)
* [DNA Germline WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-wgs.md)
* [5 Base DNA Germline Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-germline-panel.md)
* [5 Base DNA Germline WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-germline-wgs.md)

#### Germline with UMI Pipelines

* [DNA Germline Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-panel-umi.md)
* [DNA Germline WES UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-germline-wes-umi.md)
* [5 Base DNA Germline Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-germline-panel-umi.md)

#### Iterative gVCF Genotyper Pipelines

* [iGG Large Cohort](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/igg-large-cohort.md)
* [iGG Small Cohort](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/igg-small-cohort.md)

#### RNA and scRNA Pipelines

* [Illumina scRNA](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/illumina-scrna.md)
* [Illumina scRNA Perturb seq](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/illumina-scrna-perturb-seq.md)
* [Other scRNA prep](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/other-scrna-prep.md)
* [RNA Amplicon](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/rna-amplicon.md)
* [RNA Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/rna-panel.md)
* [RNA WTS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/rna-wts.md)

#### Somatic Pipelines

* [DNA Somatic Tumor-Normal Heme WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-heme-wgs.md)
* [DNA Somatic Tumor-Normal MRD](broken://pages/zopkG8EM6zEk4OP18Poh)
* [DNA Somatic Tumor-Normal Solid Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-panel.md)
* [DNA Somatic Tumor-Normal Solid WES](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-wes.md)
* [DNA Somatic Tumor-Normal Solid WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-wgs.md)
* [DNA Somatic Tumor-Only Heme WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-heme-wgs.md)
* [DNA Somatic Tumor-Only Solid Amplicon](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-amplicon.md)
* [DNA Somatic Tumor-Only Solid Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-panel.md)
* [DNA Somatic Tumor-Only Solid WES](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-wes.md)
* [DNA Somatic Tumor-Only Solid WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-wgs.md)
* [DNA Somatic Tumor-Only ctDNA Amplicon](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-ctdna-amplicon.md)
* [5 Base DNA Somatic Tumor-Normal Solid Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-panel.md)
* [5 Base DNA Somatic Tumor-Normal Solid WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-normal-solid-wgs.md)
* [5 Base DNA Somatic Tumor-Only Solid Panel](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel.md)
* [5 Base DNA Somatic Tumor-Only Solid WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-only-solid-wgs.md)

#### Somatic with UMI Pipelines

* [DNA Somatic Tumor-Normal Solid Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-panel-umi.md)
* [DNA Somatic Tumor-Normal Solid WES UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-wes-umi.md)
* [DNA Somatic Tumor-Normal Solid WGS UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-normal-solid-wgs-umi.md)
* [DNA Somatic Tumor-Only Solid Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-panel-umi.md)
* [DNA Somatic Tumor-Only Solid WES UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-wes-umi.md)
* [DNA Somatic Tumor-Only Solid WGS UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-solid-wgs-umi.md)
* [DNA Somatic Tumor-Only ctDNA Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/dna-somatic-tumor-only-ctdna-panel-umi.md)
* [5 Base DNA Somatic Tumor-Only Solid Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-only-solid-panel-umi.md)
* [5 Base DNA Somatic Tumor-Only ctDNA Panel UMI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/5-base-dna-somatic-tumor-only-ctdna-panel-umi.md)

#### TruPath Pipelines

* [Illumina TruPath Genome WGS](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-recipes/illumina-trupath-genome-wgs.md)


---

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