This is the new *CloudFormation Template Reference Guide*. Please update your bookmarks and links. For help getting started with CloudFormation, see the [AWS CloudFormation User Guide](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/Welcome.html).

# AWS::Omics::AnnotationStore
<a name="aws-resource-omics-annotationstore"></a>

**Important**  
AWS HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [AWS HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).

Creates an annotation store.

## Syntax
<a name="aws-resource-omics-annotationstore-syntax"></a>

To declare this entity in your CloudFormation template, use the following syntax:

### JSON
<a name="aws-resource-omics-annotationstore-syntax.json"></a>

```
{
  "Type" : "AWS::Omics::AnnotationStore",
  "Properties" : {
      "[Description](#cfn-omics-annotationstore-description)" : String,
      "[Name](#cfn-omics-annotationstore-name)" : String,
      "[Reference](#cfn-omics-annotationstore-reference)" : ReferenceItem,
      "[SseConfig](#cfn-omics-annotationstore-sseconfig)" : SseConfig,
      "[StoreFormat](#cfn-omics-annotationstore-storeformat)" : String,
      "[StoreOptions](#cfn-omics-annotationstore-storeoptions)" : StoreOptions,
      "[Tags](#cfn-omics-annotationstore-tags)" : {Key: Value, ...}
    }
}
```

### YAML
<a name="aws-resource-omics-annotationstore-syntax.yaml"></a>

```
Type: AWS::Omics::AnnotationStore
Properties:
  [Description](#cfn-omics-annotationstore-description): String
  [Name](#cfn-omics-annotationstore-name): String
  [Reference](#cfn-omics-annotationstore-reference): 
    ReferenceItem
  [SseConfig](#cfn-omics-annotationstore-sseconfig): 
    SseConfig
  [StoreFormat](#cfn-omics-annotationstore-storeformat): String
  [StoreOptions](#cfn-omics-annotationstore-storeoptions): 
    StoreOptions
  [Tags](#cfn-omics-annotationstore-tags): 
    Key: Value
```

## Properties
<a name="aws-resource-omics-annotationstore-properties"></a>

`Description`  <a name="cfn-omics-annotationstore-description"></a>
A description for the store.  
*Required*: No  
*Type*: String  
*Minimum*: `0`  
*Maximum*: `500`  
*Update requires*: [No interruption](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-no-interrupt)

`Name`  <a name="cfn-omics-annotationstore-name"></a>
The name of the Annotation Store.  
*Required*: Yes  
*Type*: String  
*Pattern*: `^([a-z]){1}([a-z0-9_]){2,254}`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`Reference`  <a name="cfn-omics-annotationstore-reference"></a>
The genome reference for the store's annotations.  
*Required*: No  
*Type*: [ReferenceItem](aws-properties-omics-annotationstore-referenceitem.md)  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`SseConfig`  <a name="cfn-omics-annotationstore-sseconfig"></a>
The store's server-side encryption (SSE) settings.  
*Required*: No  
*Type*: [SseConfig](aws-properties-omics-annotationstore-sseconfig.md)  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`StoreFormat`  <a name="cfn-omics-annotationstore-storeformat"></a>
The annotation file format of the store.  
*Required*: Yes  
*Type*: String  
*Allowed values*: `GFF | TSV | VCF`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`StoreOptions`  <a name="cfn-omics-annotationstore-storeoptions"></a>
File parsing options for the annotation store.  
*Required*: No  
*Type*: [StoreOptions](aws-properties-omics-annotationstore-storeoptions.md)  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`Tags`  <a name="cfn-omics-annotationstore-tags"></a>
Tags for the store.  
*Required*: No  
*Type*: Object of String  
*Pattern*: `.+`  
*Minimum*: `0`  
*Maximum*: `256`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

## Return values
<a name="aws-resource-omics-annotationstore-return-values"></a>

### Ref
<a name="aws-resource-omics-annotationstore-return-values-ref"></a>

When you pass the logical ID of this resource to the intrinsic `Ref` function, `Ref` returns the details of this resource. For example:

`{ "Ref": "AnnotationStore.Id" }``Ref` returns the id for the annotation store. 

### Fn::GetAtt
<a name="aws-resource-omics-annotationstore-return-values-fn--getatt"></a>

The `Fn::GetAtt` intrinsic function returns a value for a specified attribute of this type. The following are the available attributes and sample return values.

For more information about using the `Fn::GetAtt` intrinsic function, see [https://docs.aws.amazon.com/AWSCloudFormation/latest/TemplateReference/intrinsic-function-reference-getatt.html](https://docs.aws.amazon.com/AWSCloudFormation/latest/TemplateReference/intrinsic-function-reference-getatt.html).

#### 
<a name="aws-resource-omics-annotationstore-return-values-fn--getatt-fn--getatt"></a>

`CreationTime`  <a name="CreationTime-fn::getatt"></a>
When the store was created.

`Id`  <a name="Id-fn::getatt"></a>
The store's ID.

`Status`  <a name="Status-fn::getatt"></a>
The store's status.

`StatusMessage`  <a name="StatusMessage-fn::getatt"></a>
The store's status message.

`StoreArn`  <a name="StoreArn-fn::getatt"></a>
The store's ARN.

`StoreSizeBytes`  <a name="StoreSizeBytes-fn::getatt"></a>
The store's size in bytes.

`UpdateTime`  <a name="UpdateTime-fn::getatt"></a>
When the store was updated.

# AWS::Omics::AnnotationStore ReferenceItem
<a name="aws-properties-omics-annotationstore-referenceitem"></a>

A genome reference.

## Syntax
<a name="aws-properties-omics-annotationstore-referenceitem-syntax"></a>

To declare this entity in your CloudFormation template, use the following syntax:

### JSON
<a name="aws-properties-omics-annotationstore-referenceitem-syntax.json"></a>

```
{
  "[ReferenceArn](#cfn-omics-annotationstore-referenceitem-referencearn)" : String
}
```

### YAML
<a name="aws-properties-omics-annotationstore-referenceitem-syntax.yaml"></a>

```
  [ReferenceArn](#cfn-omics-annotationstore-referenceitem-referencearn): String
```

## Properties
<a name="aws-properties-omics-annotationstore-referenceitem-properties"></a>

`ReferenceArn`  <a name="cfn-omics-annotationstore-referenceitem-referencearn"></a>
The reference's ARN.  
*Required*: Yes  
*Type*: String  
*Pattern*: `^arn:.+$`  
*Minimum*: `1`  
*Maximum*: `127`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

# AWS::Omics::AnnotationStore SseConfig
<a name="aws-properties-omics-annotationstore-sseconfig"></a>

Server-side encryption (SSE) settings for a store.

## Syntax
<a name="aws-properties-omics-annotationstore-sseconfig-syntax"></a>

To declare this entity in your CloudFormation template, use the following syntax:

### JSON
<a name="aws-properties-omics-annotationstore-sseconfig-syntax.json"></a>

```
{
  "[KeyArn](#cfn-omics-annotationstore-sseconfig-keyarn)" : String,
  "[Type](#cfn-omics-annotationstore-sseconfig-type)" : String
}
```

### YAML
<a name="aws-properties-omics-annotationstore-sseconfig-syntax.yaml"></a>

```
  [KeyArn](#cfn-omics-annotationstore-sseconfig-keyarn): String
  [Type](#cfn-omics-annotationstore-sseconfig-type): String
```

## Properties
<a name="aws-properties-omics-annotationstore-sseconfig-properties"></a>

`KeyArn`  <a name="cfn-omics-annotationstore-sseconfig-keyarn"></a>
An encryption key ARN.  
*Required*: No  
*Type*: String  
*Pattern*: `arn:([^: ]*):([^: ]*):([^: ]*):([0-9]{12}):([^: ]*)`  
*Minimum*: `20`  
*Maximum*: `2048`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`Type`  <a name="cfn-omics-annotationstore-sseconfig-type"></a>
The encryption type.  
*Required*: Yes  
*Type*: String  
*Allowed values*: `KMS`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

# AWS::Omics::AnnotationStore StoreOptions
<a name="aws-properties-omics-annotationstore-storeoptions"></a>

The store's file parsing options.

## Syntax
<a name="aws-properties-omics-annotationstore-storeoptions-syntax"></a>

To declare this entity in your CloudFormation template, use the following syntax:

### JSON
<a name="aws-properties-omics-annotationstore-storeoptions-syntax.json"></a>

```
{
  "[TsvStoreOptions](#cfn-omics-annotationstore-storeoptions-tsvstoreoptions)" : TsvStoreOptions
}
```

### YAML
<a name="aws-properties-omics-annotationstore-storeoptions-syntax.yaml"></a>

```
  [TsvStoreOptions](#cfn-omics-annotationstore-storeoptions-tsvstoreoptions): 
    TsvStoreOptions
```

## Properties
<a name="aws-properties-omics-annotationstore-storeoptions-properties"></a>

`TsvStoreOptions`  <a name="cfn-omics-annotationstore-storeoptions-tsvstoreoptions"></a>
Formatting options for a TSV file.  
*Required*: Yes  
*Type*: [TsvStoreOptions](aws-properties-omics-annotationstore-tsvstoreoptions.md)  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

# AWS::Omics::AnnotationStore TsvStoreOptions
<a name="aws-properties-omics-annotationstore-tsvstoreoptions"></a>

The store's parsing options.

## Syntax
<a name="aws-properties-omics-annotationstore-tsvstoreoptions-syntax"></a>

To declare this entity in your CloudFormation template, use the following syntax:

### JSON
<a name="aws-properties-omics-annotationstore-tsvstoreoptions-syntax.json"></a>

```
{
  "[AnnotationType](#cfn-omics-annotationstore-tsvstoreoptions-annotationtype)" : String,
  "[FormatToHeader](#cfn-omics-annotationstore-tsvstoreoptions-formattoheader)" : {Key: Value, ...},
  "[Schema](#cfn-omics-annotationstore-tsvstoreoptions-schema)" : [ {Key: Value, ...}, ... ]
}
```

### YAML
<a name="aws-properties-omics-annotationstore-tsvstoreoptions-syntax.yaml"></a>

```
  [AnnotationType](#cfn-omics-annotationstore-tsvstoreoptions-annotationtype): String
  [FormatToHeader](#cfn-omics-annotationstore-tsvstoreoptions-formattoheader): 
    Key: Value
  [Schema](#cfn-omics-annotationstore-tsvstoreoptions-schema): 
    - 
    Key: Value
```

## Properties
<a name="aws-properties-omics-annotationstore-tsvstoreoptions-properties"></a>

`AnnotationType`  <a name="cfn-omics-annotationstore-tsvstoreoptions-annotationtype"></a>
The store's annotation type.  
*Required*: No  
*Type*: String  
*Allowed values*: `GENERIC | CHR_POS | CHR_POS_REF_ALT | CHR_START_END_ONE_BASE | CHR_START_END_REF_ALT_ONE_BASE | CHR_START_END_ZERO_BASE | CHR_START_END_REF_ALT_ZERO_BASE`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`FormatToHeader`  <a name="cfn-omics-annotationstore-tsvstoreoptions-formattoheader"></a>
The store's header key to column name mapping.  
*Required*: No  
*Type*: Object of String  
*Pattern*: `.+`  
*Minimum*: `0`  
*Maximum*: `1000`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)

`Schema`  <a name="cfn-omics-annotationstore-tsvstoreoptions-schema"></a>
The schema of an annotation store.  
*Required*: No  
*Type*: Array of Object  
*Minimum*: `1`  
*Maximum*: `5000`  
*Update requires*: [Replacement](https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-updating-stacks-update-behaviors.html#update-replacement)