Please ensure you first upload the chr1.vcf.gz and chr1.vcf.gz.tbi files to an S3 bucket that is accessible from the sBeacon deployment account. Obtain the S3 URI for the chr1.vcf.gz from the uploaded desitation. Note that, both vcf.gz and vcf.gz.tbi files must have the same prefix in S3 for this to work. Please note that, all the buckets you create in AWS are in the same region as the deployment.
Now edit the submission.json using the S3 URI of the vcf.gz file.
{
// other fields
"vcfLocations": [
"s3://<bucket>/<prefix>/chr1.vcf.gz"
],
// other fields
}You can submit this data in two ways.
You can simply copy the edited JSON content in to the API gateway /submit_dataset POST endpoint. If you're using a REST client make sure you add authorization headers before you make the request. For example, Postman supports Authorization type AWS Signature and there you can enter AWS Keys.
Alternatively, you can upload edited submission.json file to an S3 location accessible from deployment. Then you can use the file's S3 URI as follows in the API Gateway or in your REST client.
{
"s3Payload": "s3://<bucket>/<prefix>/submission.json"
}Option 2 is recommended for larger submissions with thousands of metadata entries.
Query
Schema for the query.requestParameters attribute is available at ../shared_resources/schemas/g-variants-request-parameters.json.
{
"meta": {
"apiVersion": "v2.0"
},
"query": {
"pagination": {},
"includeResultsetResponses": "HIT",
"requestedGranularity": "record",
"filters": [
],
"requestParameters": {
"assemblyId": "GRCH38",
"start": [
546801
],
"end": [
546810
],
"referenceName": "1"
}
}
}Result
Result follows the genomic variations models which has the schema presented at ../shared_resources/schemas/genomic-variation-schema.json.
{
"meta": {
"beaconId": "au.csiro-serverless.beacon",
"apiVersion": "v2.0.0",
"returnedGranularity": "record",
"receivedRequestSummary": {
"apiVersion": "v2.0",
"requestedSchemas": [],
"filters": [],
"req_params": {
"assemblyId": "GRCH38",
"start": [
546801
],
"end": [
546810
],
"referenceName": "1"
},
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"requestedGranularity": "record",
"testMode": false
},
"returnedSchemas": [
{
"entityType": "genomicVariation",
"schema": "beacon-g_variant-v2.0.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 2
},
"response": {
"resultSets": [
{
"id": "",
"setType": "",
"exists": true,
"resultsCount": 2,
"results": [
{
"variantInternalId": "R1JDSDM4CTEJNTQ2ODAyCUcJQw==",
"variation": {
"referenceBases": "G",
"alternateBases": "C",
"location": {
"interval": {
"start": {
"type": "Number",
"value": 546802
},
"end": {
"type": "Number",
"value": 546803
},
"type": "SequenceInterval"
},
"sequence_id": "GRCH38",
"type": "SequenceLocation"
},
"variantType": "SNP"
}
},
{
"variantInternalId": "R1JDSDM4CTEJNTQ2ODA1CVQJQw==",
"variation": {
"referenceBases": "T",
"alternateBases": "C",
"location": {
"interval": {
"start": {
"type": "Number",
"value": 546805
},
"end": {
"type": "Number",
"value": 546806
},
"type": "SequenceInterval"
},
"sequence_id": "GRCH38",
"type": "SequenceLocation"
},
"variantType": "SNP"
}
}
],
"resultsHandover": null
}
]
},
"beaconHandovers": []
}Query
{
"meta": {
"apiVersion": "v2.0"
},
"query": {
"requestedGranularity": "record",
"pagination": {
"limit": 1
},
"filters": []
}
}Result
{
"meta": {
"beaconId": "au.csiro-serverless.beacon",
"apiVersion": "v2.0.0",
"returnedGranularity": "record",
"receivedRequestSummary": {
"apiVersion": "v2.0",
"requestedSchemas": [],
"filters": [],
"req_params": {},
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 1
},
"requestedGranularity": "record",
"testMode": false
},
"returnedSchemas": [
{
"entityType": "individual",
"schema": "beacon-individual-v2.0.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 9
},
"response": {
"resultSets": [
{
"id": "",
"setType": "",
"exists": true,
"resultsCount": 9,
"results": [
{
"diseases": [
{
"diseaseCode": {
"id": "SNOMED:56265001",
"label": "Heart disease (disorder)"
}
}
],
"ethnicity": {
"id": "SNOMED:17789004",
"label": "Papuans"
},
"exposures": "",
"geographicOrigin": {
"id": "SNOMED:223713009",
"label": "Argentina"
},
"id": "UNQ_1-6",
"info": "",
"interventionsOrProcedures": [
{
"procedureCode": {
"id": "NCIT:C93025"
}
}
],
"karyotypicSex": "XX",
"measures": "",
"pedigrees": "",
"phenotypicFeatures": "",
"sex": {
"id": "SNOMED:248152002",
"label": "Female"
},
"treatments": ""
}
],
"resultsHandover": null
}
]
},
"beaconHandovers": []
}Query
{
"query": {
"filters": [
{
"id": "SNOMED:223688001"
}
],
"requestedGranularity": "count"
},
"meta": {
"apiVersion": "v2.0"
}
}Result
{
"meta": {
"beaconId": "au.csiro-serverless.beacon",
"apiVersion": "v2.0.0",
"returnedGranularity": "count",
"receivedRequestSummary": {
"apiVersion": "v2.0",
"requestedSchemas": [],
"filters": [
{
"id": "SNOMED:223688001"
}
],
"req_params": {},
"includeResultsetResponses": "HIT",
"pagination": {
"skip": 0,
"limit": 10
},
"requestedGranularity": "count",
"testMode": false
},
"returnedSchemas": [
{
"entityType": "individual",
"schema": "beacon-individual-v2.0.0"
}
]
},
"responseSummary": {
"exists": true,
"numTotalResults": 4
},
"beaconHandovers": []
}