Creating HealthOmics variant stores

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The following topics describe how to create HealthOmics variant stores using the console and the API.

Creating a variant store using the console

You can create a variant store using the HealthOmics console.

1. Open the HealthOmics console https://console.aws.amazon.com/omics/.

2. In the left navigation pane, choose Variant stores.

3. On the Create variant store page, provide the following information

   • Variant store name - A unique name for this store.

   • Description (optional) - A description of this variant store.

   • Reference genome - The reference genome for this variant store.

   • Data Encryption - Choose whether you want data encryption to be owned and managed by AWS or by yourself.

   • Tags (optional) - Provide up to 50 tags for this variant store.

4. Choose Create variant store.

Creating a variant store using the API

Use HealthOmics CreateVariantStore API operation to create variant stores. You can also perform this operation with the AWS CLI.

To create a variant store, you provide a name for the store and the ARN of a reference store. The variant store is ready to ingest data when its status changes to READY.

The following example uses the AWS CLI to create a variant store.

aws omics create-variant-store --name myvariantstore \
    --reference referenceArn="arn:aws:omics:us-west-2:555555555555:referenceStore/123456789/reference/5987565360"

To confirm the creation of your variant store, you receive the following response.

{
    "creationTime": "2022-11-03T18:19:52.296368+00:00",
    "id": "45aeb91d5678",
    "name": "myvariantstore",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:555555555555:referenceStore/123456789/reference/5987565360"
    },
    "status": "CREATING"
}   

To learn more about a variant store, use the get-variant-store API.

aws omics get-variant-store --name myvariantstore

You receive the following response.

{
    "id": "45aeb91d5678",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:555555555555:referenceStore/123456789/reference/5987565360"
    },
    "status": "ACTIVE",
    "storeArn": "arn:aws:omics:us-west-2:555555555555:variantStore/myvariantstore",
    "name": "myvariantstore",
    "creationTime": "2022-11-03T18:19:52.296368+00:00",
    "updateTime": "2022-11-03T18:30:56.272792+00:00",
    "tags": {},
    "storeSizeBytes": 0
}    

To view all variant stores associated with an account, use the list-variant-stores API.

aws omics list-variant-stores  

You receive a response that lists all variant stores, along with their IDs, statuses, and other details, as shown in the following example response.

{
    "variantStores": [
        {
            "id": "45aeb91d5678",
            "reference": {
                "referenceArn": "arn:aws:omics:us-west-2:55555555555:referenceStore/5506874698"
            },
            "status": "ACTIVE",
            "storeArn": "arn:aws:omics:us-west-2:55555555555:variantStore/new_variant_store",
            "name": "variantstore",
            "creationTime": "2022-11-03T18:19:52.296368+00:00",
            "updateTime": "2022-11-03T18:30:56.272792+00:00",
            "statusMessage": "",
            "storeSizeBytes": 141526
        }
    ]
}  

You can also filter the responses for the list-variant-stores API based on statuses or other criteria.

VCF Files imported into analytic stores created on or after May 15, 2023 have defined schemas for Variant Effect Predictor (VEP) annotations. This makes it easier to query and parse imported VCF data. The change doesn't impact stores created before May 15, 2023, except if the annotation fields parameter is included in the API or CLI call. For these stores, using the annotation fields parameter will cause the request to fail.