# Running queries on HealthOmics variant stores
<a name="analytics-run-queries"></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](variant-store-availability-change.md).

You can perform queries on your variant store using Amazon Athena. Note that genomic coordinates in variant and annotation stores are represented as zero-based, half-closed half-open intervals.

## Run a simple query using the Athena console
<a name="run-queries-athena-simple"></a>

The following example shows how to run a simple query.

1. Open the Athena Query editor: [Athena Query editor](https://console.aws.amazon.com//athena)

1. Under **Workgroup**, select the workgroup that you created during setup.

1. Verify that **Data source** is **AwsDataCatalog**.

1. For **Database**, select the database resource link that you created during the Lake Formation setup.

1. Copy the following query into the **Query Editor ** under the **Query 1** tab:

   ```
   SELECT * from omicsvariants limit 10
   ```

1. Choose **Run** to run the query. The console populates the results table with the first 10 rows of the **omicsvariants** table.

## Run a complex query using the Athena console
<a name="run-queries-athena-complex"></a>

The following example shows how to run a complex query. To run this query, import `ClinVar` into the annotation store.

**Run a complex query**

1. Open the Athena Query editor: [Athena Query editor](https://console.aws.amazon.com//athena)

1. Under**Workgroup**, select the workgroup that you created during setup.

1. Verify that **Data source** is **AwsDataCatalog**.

1. For **Database**, select the database resource link that you created during the Lake Formation setup.

1. Choose the **\$1** at the top right to create a new query tab named **Query 2**.

1. Copy the following query into the **Query Editor ** under the **Query 2** tab:

   ```
   SELECT variants.sampleid,
     variants.contigname,
     variants.start,
     variants."end",
     variants.referenceallele,
     variants.alternatealleles,
     variants.attributes AS variant_attributes,
     clinvar.attributes AS clinvar_attributes  
   FROM omicsvariants as variants 
   INNER JOIN omicsannotations as clinvar ON 
     variants.contigname=CONCAT('chr',clinvar.contigname) 
     AND variants.start=clinvar.start 
     AND variants."end"=clinvar."end" 
     AND variants.referenceallele=clinvar.referenceallele 
     AND variants.alternatealleles=clinvar.alternatealleles 
   WHERE clinvar.attributes['CLNSIG']='Likely_pathogenic'
   ```

1. Choose **Run** to start running the query.