> 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/annotation/v3.27/introduction/getting-started-dragen.md). # Getting Started with DRAGEN ### Overview Illumina Connected Annotations is bundled with DRAGEN and provides comprehensive variant annotation capabilities. You can annotate VCF files either: * Automatically through DRAGEN pipeline parameters * Manually using the standalone Illumina Connected Annotations tool {% hint style="info" %} **Key Requirements** Before annotating variants, you must: 1. Configure credentials for premium data sources 2. Download annotation data files 3. Specify the data location when running DRAGEN or the standalone tool {% endhint %} ### Installation Paths The annotation binaries location depends on your DRAGEN environment: | Environment | Nirvana Path | Resource Path | | -------------- | --------------------------------------------- | ---------------------------------------------------- | | **On-Premise** | `/opt/dragen//share/nirvana/` | `/opt/dragen//resources/annotation/` | | **Cloud** | `/opt/edico/share/nirvana/` | `/opt/edico/resources/annotation/` | **Available binaries:** * `Nirvana`: Illumina Connected Annotations tool * `DataManager`: Annotation data download manager {% hint style="warning" %} **Platform Compatibility** `Nirvana` and `DataManager` are compatible with CentOS 7, Oracle 8, and other modern Linux distributions using x64 processors. {% endhint %} ### Automated Setup Script For a streamlined setup experience, use the Annotation Setup script (download below) which automates all the configuration steps: {% file src="/files/I0Dj4V3erjdQwMCUaerS" %} ```bash # Download the provisioning script wget https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/utilities/resources/annotation_setup.sh # Make it executable chmod +x annotation_setup.sh # Run interactively (guided setup) ./annotation_setup.sh # Or run with command-line options ./annotation_setup.sh \ --dragen-path /opt/dragen/4.5.0 \ --data-dir /data/nirvana_data ``` **Features:** * **Interactive mode**: Step-by-step guidance for credential setup and data download * **CLI mode**: Fully automated for scripting and CI/CD pipelines * **Automatic credential detection**: Uses environment variables or prompts for credentials * **Multi-download support**: Download multiple assemblies and annotation types in one run * **Dry-run mode**: Preview commands without downloading (use `--dry-run`) ### Quick Start Reference #### On-Premise DRAGEN ```bash # Set DRAGEN serial number as environment variable export DRAGEN_SERIAL_NUMBER="$(dragen_info -qs)" # Download annotation data (credentials auto-detected from environment) /opt/dragen//share/nirvana/DataManager download \ -r GRCh38 \ --dir /data/nirvana_data \ --versions-config /opt/dragen//resources/annotation/all_annotations_GRCh38.json /opt/dragen//share/nirvana/DataManager download \ -r GRCh38 \ --dir /data/nirvana_data \ --versions-config /opt/dragen//resources/annotation/tmb_annotations_GRCh38.json # Annotate variants via DRAGEN dragen \ --enable-variant-annotation true \ --variant-annotation-data /data/nirvana_data \ --variant-annotation-assembly GRCh38 \ [... other parameters ...] ``` #### Cloud DRAGEN ```bash # Download annotation data using DRAGEN API key file /opt/edico/share/nirvana/DataManager download \ -r GRCh38 \ --api-key-file /path/to/dragen_api_key.txt \ --dir /data/nirvana_data \ --versions-config /opt/edico/resources/annotation/all_annotations_GRCh38.json /opt/edico/share/nirvana/DataManager download \ -r GRCh38 \ --api-key-file /path/to/dragen_api_key.txt \ --dir /data/nirvana_data \ --versions-config /opt/edico/resources/annotation/tmb_annotations_GRCh38.json # Annotate variants via DRAGEN dragen \ --enable-variant-annotation true \ --variant-annotation-data /data/nirvana_data \ --variant-annotation-assembly GRCh38 \ [... other parameters ...] ``` {% hint style="info" %} **Alternative Cloud Option** If you already have a DRAGEN `--lic-credentials` file, you can use it directly: ```bash /opt/edico/share/nirvana/DataManager download \ -r GRCh38 \ --lic-credentials /path/to/lic_credentials_file \ --dir /data/nirvana_data \ --versions-config /opt/edico/resources/annotation/all_annotations_GRCh38.json /opt/edico/share/nirvana/DataManager download \ -r GRCh38 \ --lic-credentials /path/to/lic_credentials_file \ --dir /data/nirvana_data \ --versions-config /opt/edico/resources/annotation/tmb_annotations_GRCh38.json ``` {% endhint %} ### Detailed Instructions #### Step 1: Configure Credentials To access premium annotation data sources, you need to provide credentials. The system supports multiple authentication methods and will automatically search for credentials in several locations. **Supported Authentication Methods** The annotation tools support the following authentication methods: | Authentication Method | Use Case | Environment Variables | Command-Line Options | | ------------------------ | --------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------ | | **DRAGEN Serial Number** | On-premise DRAGEN servers | `DRAGEN_SERIAL_NUMBER` | `--credentials-file` | | **DRAGEN API Key** | DRAGEN cloud/platform deployments |

DRAGEN\_API\_KEY\_VALUE
DRAGEN\_API\_KEY\_FILE (path)

|

--api-key-file
--credentials-file

| | **BYOL Credentials** | Cloud DRAGEN users |

NIRVANA\_API\_KEY + NIRVANA\_API\_SECRET
DRAGEN\_LICENSE\_CREDENTIALS\_FILE (path)

|

--lic-credentials
--credentials-file

| {% hint style="info" %} **Credential Priority** If multiple authentication methods are configured, the system will use them in this priority order: 1. DRAGEN Serial Number 2. BYOL Credentials (ApiKey/ApiSecret) 3. DRAGEN API Key You only need to provide **one** authentication method. {% endhint %} **Credential Configuration Options** You can configure credentials using any of these methods: **Option 1: Default credentials directory** **Option 2: Explicit file paths** **Option 3: Environment variables** **Option 1: Default Credentials Directory** Automatically look for credentials in `~/.ilmnAnnotations/` directory: | File Name | Purpose | Format | | ------------------------ | -------------------------------------- | --------------- | | `credentials.json` | Main credentials file (all auth types) | JSON | | `dragen_api_key.txt` | DRAGEN API key only | Plain text | | `dragen_credentials.txt` | BYOL credentials (ApiKey/ApiSecret) | Key-value pairs | **Option 2: Explicit File Paths** You can specify credential file locations using command-line arguments: | Tool | Argument | Description | | ----------- | ------------------------------------------ | --------------------------------------------------- | | DataManager | `--credentials-file ` or `-l ` | Path to credentials.json | | DataManager | `--api-key-file ` | Path to raw API key file | | DataManager | `--lic-credentials ` | Path to license credentials file (key-value format) | **Option 3: Environment Variables** Set environment variables for automatic credential detection: | Environment Variable | Description | Example | | --------------------------------- | ---------------------------------- | --------------------------------- | | `MY_ILLUMINA_API_KEY` | MyIllumina API key | `your-api-key` | | `DRAGEN_SERIAL_NUMBER` | DRAGEN serial number | `ABCD1234` | | `DRAGEN_API_KEY_VALUE` | DRAGEN API key value | `your-dragen-api-key` | | `DRAGEN_API_KEY_FILE` | Path to DRAGEN API key file | `/path/to/api_key.txt` | | `NIRVANA_API_KEY` | BYOL API key (user\_id) | `your-user-id` | | `NIRVANA_API_SECRET` | BYOL API secret (password) | `your-password` | | `DRAGEN_LICENSE_CREDENTIALS_FILE` | Path to DRAGEN license credentials | `/path/to/dragen_credentials.txt` | **Examples:** ```bash **Setting environment variables:** # DRAGEN Serial Number (on-premise) export DRAGEN_SERIAL_NUMBER="ABCD1234" # DRAGEN API Key (cloud/platform) export DRAGEN_API_KEY_VALUE="your-dragen-api-key" # or point to a file export DRAGEN_API_KEY_FILE="/path/to/api_key.txt" # BYOL Credentials (cloud) export NIRVANA_API_KEY="your-user-id" export NIRVANA_API_SECRET="your-password" # or point to a file export DRAGEN_LICENSE_CREDENTIALS_FILE="/path/to/dragen_credentials.txt" ``` *** **Credentials File Formats** **Format 1: credentials.json (Recommended)** The `credentials.json` file supports all authentication methods in a single file: **On-Premise DRAGEN:** ```json { "DragenSerialNo": "" } ``` **Cloud DRAGEN (BYOL):** ```json { "ApiKey": "", "ApiSecret": "" } ``` **MyIllumina Platform:** Basic, without access to premium data: ```json { "MyIlluminaApiKey": "" } ``` **All supported fields:** ```json { "MyIlluminaApiKey": "", "DragenSerialNo": "", "ApiKey": "", "ApiSecret": "", "DragenApiKey": "" } ``` **Format 2: dragen\_api\_key.txt** A plain text file containing only the DRAGEN API key: ``` your-dragen-api-key-value ``` **Format 3: dragen\_credentials.txt** A key-value pair file for BYOL credentials: ``` credentials-1= credentials-2= ``` *** **Setting Up Credentials by Environment** **On-Premise DRAGEN** **Required credential:** DRAGEN Serial Number **Obtaining your DRAGEN serial number:** If you have a single DRAGEN version: ```shell dragen_info -s ``` If you have multiple DRAGEN versions: ```shell # List available versions dragen_versions # Get serial number for specific version /opt/dragen//bin/dragen_info -s ``` **Creating credentials.json:** ```bash # Manual method cat > ~/.ilmnAnnotations/credentials.json << EOF { "DragenSerialNo": "$(dragen_info -qs)" } EOF ``` Or using environment variable: ```bash export DRAGEN_SERIAL_NUMBER="$(dragen_info -qs)" ``` **Cloud DRAGEN** {% hint style="info" %} **Cloud users do not have a DRAGEN serial number.** Active DRAGEN cloud users are automatically eligible for premium resources using BYOL credentials or DRAGEN API keys. {% endhint %} **Required credentials:** BYOL ApiKey/ApiSecret **or** DRAGEN API Key **Method 1: Using DRAGEN API Key** If you have a DRAGEN API key, you can use it directly: ```bash # Save to default location cat > ~/.ilmnAnnotations/dragen_api_key.txt << EOF your-dragen-api-key-value EOF ``` Or set as an environment variable: ```bash export DRAGEN_API_KEY_VALUE="your-dragen-api-key-value" ``` **Method 2: Use existing `--lic-credentials` file directly** If you run DRAGEN with `--lic-credentials `, you can use the same file directly with DataManager and Nirvana: ``` credentials-1= credentials-2= ``` **Using the license credentials file:** ```bash # With DataManager //DataManager download --lic-credentials /path/to/lic_credentials_file ``` **Optional: Convert to credentials.json** (if you prefer the JSON format): ```bash cat > ~/.ilmnAnnotations/credentials.json << EOF { "ApiKey": "$(awk -F' = ' '/^credentials-1/ {print $2}' /path/to/lic_credentials_file)", "ApiSecret": "$(awk -F' = ' '/^credentials-2/ {print $2}' /path/to/lic_credentials_file)" } EOF ``` *** {% hint style="info" %} **Troubleshooting** If you encounter authentication errors: 1. Verify credentials are in the correct format 2. Check file permissions (credentials files should be readable) 3. Ensure at least one authentication method is configured 4. Try specifying the credentials file path explicitly with `--credentials-file` {% endhint %} #### Step 2: Download Annotation Data Use the `DataManager` tool to download required annotation data sources. {% hint style="info" %} For complete DataManager documentation, see the [DataManager guide](https://github.com/illumina-swi/annotations-docs/tree/stage-release-4.0/docs/utilities/data-manager/README.md). {% endhint %} **Available Annotation Configurations** Configuration files are located in the resources directory (see [Installation Paths](#installation-paths) above): | Configuration File | Assembly | Use Case | DRAGEN Parameter | | ------------------------------------------ | -------- | ----------------------- | ----------------------------------- | | `all_annotations_GRCh37.json` | GRCh37 | Full variant annotation | `--enable-variant-annotation true` | | `all_annotations_GRCh38.json` | GRCh38 | Full variant annotation | `--enable-variant-annotation true` | | `germline_tagging_annotations_GRCh37.json` | GRCh37 | Germline tagging | `--vc-enable-germline-tagging true` | | `germline_tagging_annotations_GRCh38.json` | GRCh38 | Germline tagging | `--vc-enable-germline-tagging true` | | `tmb_annotations_GRCh37.json` | GRCh37 | Tumor Mutational Burden | `--enable-tmb true` | | `tmb_annotations_GRCh38.json` | GRCh38 | Tumor Mutational Burden | `--enable-tmb true` | **Important Notes** * TMB annotation files include germline tagging data. If you download TMB annotations, you don't need to separately download germline tagging annotations. * Running DRAGEN with `--enable-tmb true` requires TMB annotation data. * Running DRAGEN with `--vc-enable-germline-tagging true` requires germline tagging annotation data. * Missing required data will cause DRAGEN to fail with an error. ::: **Download Commands** ```bash //DataManager download \ -r \ --credentials-file \ --dir \ --versions-config /opt/dragen//resources/annotation/ ``` **Parameters:** * ``: `GRCh37` or `GRCh38` * ``: Path to your credentials file from Step 1 * ``: Destination directory for annotation files * ``: One of the configuration files listed above {% hint style="info" %} **Storage Best Practice** Use the same data directory for all configuration files. This consolidated location will be used with the `--variant-annotation-data` parameter when running DRAGEN. {% endhint %} **Download Example** Example command for full GRCh38 annotations: ```shell //DataManager download \ -r GRCh38 \ --credentials-file /home/user/credentials.json \ --dir /data/nirvana_data \ --versions-config /opt/dragen/4.4.3/resources/annotation/all_annotations_GRCh38.json ``` **Expected output:** ```shell --------------------------------------------------------------------------- DataManager (c) 2025 Illumina, Inc. 3.27.0 --------------------------------------------------------------------------- Fetching download information... Syncing local files with requested files Starting download of 40 files using 4 threads... # File Name Source Version Local Size Remote Size MD5 Hash Status ------------------------------------------------------------------------------------------------------------------------------------------ 35 Homo_sapiens.GRCh37.Nirvana... GenomeAss... GRCh37.p13 232.3 MB 0.8 GB 9065784e62b5c8039f189e84cd90fe97 Downloading 30% 29 PrimateAI_0.2.esa PrimateAI 0.2 134.0 MB 169.7 MB 576c4146c5a0f87e498fd92170682ee6 Downloading 79% 42 DANN_20200205.gsa DANN 20200205 254.6 MB 3.8 GB 9b76948a939e86e2e24360cf2a953e77 Downloading 7% 41 Gerp_20110522.gsa Gerp 20110522 263.6 MB 3.1 GB b86e1734bb6ab685149566a3ae71fc83 Downloading 8% 12 UcscCpgIsland_20200322.mroi UcscCpgIs... 20200322 0 B 1.0 MB 5187291ab3791a2cf6e0d5a89ce0cac7 Missing 0% 1 MITOMAP_SV_20200819.nsi mitomap 20200819 0 B 1.7 KB 323e4227ceed4d240b61ee0a13602a28 Missing 0% 18 ClinVarPreview_preview_2025... clinvar-p... 20250601 0 B 2.5 MB 72d7ed870bfe596c27a5752c62524f6f Missing 0% 43 dbSNP_157.nsa dbSNP 157 0 B 7.3 GB e5dab1c73f6d8195e73c67313aa7089c Missing 0% 33 gnomAD_exome_2.1.nsa gnomad-exome 2.1 0 B 0.5 GB be77803d9d7804d543a52f4158a5eb80 Missing 0% 17 ClinVar_20250601.nsi clinvar 20250601 0 B 2.3 MB ae4a3a1b4288dfe53e0107d581e5a22d Missing 0% 21 gnomAD_LCR_2.1.lcr gnomad 2.1 0 B 7.5 MB 601f94ba374c2942d5ff8ea2774308e1 Missing 0% 27 ClinVarPreview_preview_2025... clinvar-p... 20250601 0 B 145.5 MB c651b1922087b753db9ec20691bffddf Missing 0% 4 ClinGen_Dosage_Sensitivity_... clingen 20250815 0 B 10.4 KB f9c2dce4b320919601a78ff580bf6b92 Missing 0% 38 phyloP_hg19.npd phylopScore hg19 0 B 1.4 GB 023f0a72c4b4678c88cad7f3c46e3b6e Missing 0% 44 gnomAD_2.1.nsa gnomad 2.1 0 B 9.7 GB 2ae0dd89ee52d86296a4e8483d04a2ab Missing 0% 34 PrimateAI-3D_1.0.esa primateAI-3D 1.0 0 B 0.7 GB 8b7b89c01a208bfd670cff125ac2c0bc Missing 0% 10 gnomAD_gene_scores_4.1.nga gnomad 4.1 0 B 398.1 KB 684a96c10d6cb00111ab6e8eef3d3ab2 Missing 0% 22 gnomAD_SV_2.1.nsi gnomad 2.1 0 B 12.2 MB fc5d05b27bf0f99d6a0ed7cea2326ae2 Missing 0% 31 COSMIC_102.esa cosmic 102 0 B 329.0 MB dbd550f01e9d51aae5af22f9f265c66c Missing 0% 26 ClinVar_20250601.nsa clinvar 20250601 0 B 109.1 MB 6879431766846ddd42060632bb748840 Missing 0% 30 dbSNP_151_globalMinor.nsa globalAllele 151 0 B 277.3 MB 1705968d7af569c509005b43e1bbace5 Missing 0% 3 ClinGen_Dosage_Sensitivity_... clingen 20250815 0 B 8.7 KB 9c134d1d321dbb9cb95fa868266aab84 Missing 0% 24 GRCh37.RefSeq.ndb RefSeq 105.202... 0 B 50.2 MB de70384b18e82e983e138de610b9a60b Missing 0% 9 MITOMAP_20200819.nsa mitomap 20200819 0 B 142.7 KB 66ac99931479e7be721777f72c492a72 Missing 0% 14 1000_Genomes_Project_(SV)_P... oneKg Phase 3... 0 B 1.2 MB 71b9893cf8dceb9dcb9ccaa8568a786e Missing 0% 11 ClinGen_20160414.nsi clingen (... 20160414 0 B 448.6 KB c879c32cd713ea114ab6645ad136865c Missing 0% 40 TOPMed_freeze_5.nsa TOPMed freeze_5 0 B 1.9 GB 7091ebf36a049645e4d27dd4b89adf08 Missing 0% 37 PromoterAI_1.1.esa PromoterAI 1.1 0 B 1.3 GB 63740b952fc26dbb9b0b9f0177549220 Missing 0% 2 Cosmic_Cancer_Gene_Census_1... cosmic 102 0 B 2.3 KB 2d1bdfa6a1d2cd71eb5af655fcd10bc1 Missing 0% 36 1000_Genomes_Project_Phase_... oneKg Phase 3... 0 B 0.9 GB 0d3b5b0324eec691148b21508b431bfe Missing 0% 39 SpliceAi_1.3.esa spliceAI 1.3 0 B 1.5 GB d8689daa7f8a0354e3e6808c25f3096d Missing 0% 32 AlphaMissense_1.0.nsa alphaMiss... 1.0 0 B 500.0 MB 466610add1739014e8776ac28d9a6ad5 Missing 0% 16 OMIM_20250815.ega omim 20250815 0 B 1.6 MB 68219a4695860a96341b262015a8288c Missing 0% 6 ClinGen_disease_validity_cu... clingen 20250815 0 B 56.7 KB 63c1166d7bd43973140e218dc8f4127c Missing 0% 5 COSMIC_GeneFusions_102.efj cosmic 102 0 B 45.5 KB 8bcc682bcbbdd123c33e140b06be90e7 Missing 0% 28 REVEL_20200205.nsa REVEL 20200205 0 B 166.2 MB 22b81c6e8bac88bf5ebea630d87bd99f Missing 0% 15 1000_Genomes_Project_Phase_... oneKg Phase 3... 0 B 1.4 MB a695d7a0d21bcd3fa897bfa68630f2a0 Missing 0% 25 GRCh37.Ensembl.ndb Ensembl 110 71.8 MB 71.8 MB 26a66394fd82411658e117d765f9231f Downloaded 100% 7 MultiZ100Way_20150427.pcs MultiZ100Way 20150427 59.4 KB 59.4 KB 1f4a5d1592f96c1a3ca489d3aa9b9618 Downloaded 100% 8 GeneSymbols.ndb HGNC 20240603 134.0 KB 134.0 KB 153fe33bc4d7839257d81db7a3914fe7 Downloaded 100% 20 GME_20160618.nsa GME 20160618 3.6 MB 3.6 MB 313ca98c770ed69383a8b7e78abd19a7 UpToDate 100% 23 ABRaOM_SABE_609_exomes.nsa ABRaOM SABE_60... 16.4 MB 16.4 MB 2670632355457cde4d6f4d62b9b91f58 UpToDate 100% 13 DECIPHER_201509.nsi DECIPHER 201509 1.1 MB 1.1 MB 784e71f98aff7d30ed17194a490561ae UpToDate 100% 19 FusionCatcher_1.33.gfs FusionCat... 1.33 3.5 MB 3.5 MB 9eaf6a33d967dfa34fb1d0e76d63fd50 UpToDate 100% ------------------------------------------------------------------------------------------------------------------------------------------ Total=44(34.6 GB), Failed=0, Downloading=4, Completed=7(1.0 GB) | Speed=38.4 MB/s, Progress=3% | Elapsed=00:25, ETA=14:56 ``` **Example completion message:** ```shell Summary written to /data/nirvana_data/download_summary.json Table written to /data/nirvana_data/download_summary.txt Peak memory usage: 293.1 MB Time: 00:14:08.6 ``` #### Step 3: Annotate Variants Once credentials are configured and data is downloaded, you can annotate variants through DRAGEN or the standalone tool. **Option A: Annotate via DRAGEN Pipeline** Add these parameters to your DRAGEN command: | Parameter | Value | Description | | ------------------------------- | ------------------------------------ | ------------------------------------------------------------------------------------------------------ | | `--enable-variant-annotation` | `true` | Enables variant annotation | | `--variant-annotation-data` | `/path/to/data/directory` | Location of downloaded annotation files | | `--variant-annotation-assembly` | `GRCh37` or `GRCh38` | Reference genome assembly (use GRCh37 for hg19) | | `--annotation-data-config` | `/path/to/data/versions-config-json` | File path to annotation data config (json) file, if this is not set, embedded data config will be used | | `--variant-annotation-assembly` | `true` | Set Nirvana output format to VCF(optional) | **Example:** ```bash dragen \ --enable-variant-annotation true \ --variant-annotation-data /data/nirvana_data \ --variant-annotation-assembly GRCh38 \ --annotation-data-config /opt/dragen//resources/annotation/latest_annotations_GRCh38.json \ --variant-annotation-enable-vcf-output true \ [... other DRAGEN parameters ...] ``` **Option B: Annotate via Standalone Tool** Use the standalone `Nirvana` tool to annotate existing VCF files. {% hint style="info" %} For complete annotation options, see the [Illumina Connected Annotations guide](https://github.com/illumina-swi/annotations-docs/tree/stage-release-4.0/docs/introduction/getting-started/README.md#the-illumina-connected-annotations-command-line). {% endhint %} ```shell //Nirvana \ -i \ -o \ -c /Cache \ -r /References/Homo_sapiens.GRCh38.Nirvana.dat \ --sd /SupplementaryAnnotation/GRCh38 \ -l \ --versions-config /opt/dragen//resources/annotation/all_annotations_GRCh38.json ``` **Parameters:** | Option | Description | Example | | ------------------- | ----------------------------------------- | --------------------------------------------------------------- | | `-i` | Input VCF file (uncompressed or bgzipped) | `input.vcf.gz` | | `-o` | Output file prefix | `output` | | `-c` | Cache directory | `/data/nirvana_data/Cache` | | `-r` | Reference file | `/data/nirvana_data/References/Homo_sapiens.GRCh38.Nirvana.dat` | | `--sd` | Supplementary annotation directory | `/data/nirvana_data/SupplementaryAnnotation/GRCh38` | | `-l` | Credentials file | `credentials.json` | | `--versions-config` | Version configuration file | Path from resources directory | **Example output:** ```shell --------------------------------------------------------------------------- Illumina Connected Annotations (c) 2024 Illumina, Inc. 3.27.0 --------------------------------------------------------------------------- Data Source Type Status Comments --------------------------------------------------------------------------- DANN Score Loaded 20200205 Ensembl GeneModels Loaded 112 ... spliceAI SmallVariant Loaded 1.3 --------------------------------------------------------------------------- Summary Time Percent --------------------------------------------------------------------------- Initialization 00:00:11.7 84.9 % Annotation 00:00:02.0 14.4 % --------------------------------------------------------------------------- Gross Annotation rate: 718.84 positions/sec Peak memory usage: 5.867 GB Time: 00:00:13.8 ``` ### Output Formats #### JSON Output (Default) Illumina Connected Annotations produces JSON output by default. This format provides comprehensive annotation information. **Documentation:** [Illumina Connected Annotations JSON Format](/annotation/v3.27/file-formats/illumina-annotator-json-file-format.md) #### VCF Output (Optional) Add `--output-format vcf` to generate VCF output. Note that VCF format has limited annotation capabilities compared to JSON. **Documentation:** [Illumina Connected Annotations VCF Format](/annotation/v3.27/file-formats/illumina-annotator-vcf-file-format.md) ### Version History | DRAGEN Version | Annotations Version | AI Annotations | Documentation | Data Utility | | ------------------------ | ------------------- | --------------------- | ---------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | | 4.5 | 3.27.0 | spliceAI, primateAI3D | [3.27](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.27/) | [Data Manager](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.27/utilities/data-manager) | | 4.4 | 3.25.1 | spliceAI, primateAI3D | [3.25](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.25/) | [Data Manager](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.25/utilities/data-manager) | | 4.3 | 3.23 | spliceAI, primateAI3D | [3.23](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.23/) | [Downloader](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/3.23/introduction/getting-started#downloading-the-data-files) | | 3.9, 3.10, 4.0, 4.1, 4.2 | 3.16.1 | spliceAI, primateAI | [3.16](https://illumina.github.io/NirvanaDocumentation/3.16/) | [Downloader](https://illumina.github.io/NirvanaDocumentation/3.16/introduction/getting-started#downloading-the-data-files) | | 3.8 | 3.14 | spliceAI, primateAI | [3.14](https://illumina.github.io/NirvanaDocumentation/3.14/) | [Downloader](https://illumina.github.io/NirvanaDocumentation/3.14/introduction/getting-started#downloading-the-data-files) | | 3.6, 3.7 | 3.9.0 | spliceAI, primateAI | Not Available | Not Available | | 3.5 | 3.6.0 | spliceAI, primateAI | Not Available | Not Available | {% hint style="info" %} Annotations binaries have been included with DRAGEN since v3.5. Newer versions are backward compatible and can annotate output files from older DRAGEN releases. {% endhint %} --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/annotation/v3.27/introduction/getting-started-dragen.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.