> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/annotation/software-functionality/command-line-parameters.md).

# Command Line Parameters

DRAGEN Annotation supports the following command-line parameters:

| Option(s)                             | Description                                                                                     |
| ------------------------------------- | ----------------------------------------------------------------------------------------------- |
| `--cache, -c`                         | Input cache directory                                                                           |
| `--in, -i`                            | Input VCF path                                                                                  |
| `--tsv`                               | Input TSV path                                                                                  |
| `--out, -o`                           | Output file prefix (.json.gz will be added to complete the file path)                           |
| `--ref, -r`                           | Input compressed reference sequence path                                                        |
| `--sd`                                | Input supplementary annotation directory                                                        |
| `--sources, -s`                       | Annotation data sources to be used (comma-separated list of supported tags)                     |
| `--credentials-file, -l`              | File path to user credentials (default: `~/.ilmnAnnotations/credentials.json`)                  |
| `--versions-config`                   | Annotation version config file (default: `~/.ilmnAnnotation/<assembly>_annotation_config.json`) |
| `--ignore-license-error`              | Ignore error due to invalid license and skip related data sources                               |
| `--force-mt`                          | Forces annotation of mitochondrial variants                                                     |
| `--legacy-vids`                       | Enables support for legacy VIDs                                                                 |
| `--enable-dq`                         | Report DQ from VCF samples field                                                                |
| `--enable-bidirectional-fusions`      | Enables support for bidirectional gene fusions                                                  |
| `--disable-junction-preservation`     | Disable junction preserving functional annotation                                               |
| `--str`                               | User-provided STR annotation TSV file                                                           |
| `--vcf-info`                          | Additional VCF info field keys (comma-separated) desired in the output                          |
| `--vcf-sample-info`                   | Additional VCF format field keys (comma-separated) desired in the output                        |
| `--sa-cutoff`                         | SVs ≥ this value will not have supplementary annotations                                        |
| `--simple-nomenclature-cutoff-length` | SVs ≥ this value will have simple nomenclature annotation (default: 1000)                       |
| `--output-format`                     | Output file format (options: `json`, `vcf`)                                                     |
| `--help, -h`                          | Displays the help menu                                                                          |
| `--version, -v`                       | Displays the version                                                                            |

Most of the options are self explanatory. In the following sections, we provide more details about some that may not be obvious:

## `--force-mt`

For `hg19` genome assembly, the default behavior is to skip annotating the mitochondrial chromosome. This can be overridden using this flag.

## `--disable-junction-preservation`

By default, junction preserving behavior as described in [Junction Preserving Annotation](/annotation/core-functionality/junction-preserving.md) is enabled. This flag can turn it off.

## `--vcf-info`

DRAGEN Annotation does not pass every VCF INFO field to JSON output. Use this parameter to include specific fields. Separate multiple keys with commas.

## `--vcf-sample-info`

DRAGEN Annotation does not pass every sample field to JSON output. Use this parameter to include specific fields. Separate multiple keys with commas.


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