diff --git a/beacon.md b/beacon.md index 63fb1319..00fb3189 100644 --- a/beacon.md +++ b/beacon.md @@ -1,5 +1,5 @@ -# Beacon API Specification v1.0.0 +# Beacon API Specification v1.1.0 Beacon is a web service for genetic data sharing. Beacon permits simple queries regarding the presence or absence of a specified variant in a given dataset. This is the key idea behind Beacon, by allowing these queries Beacon makes the data discoverable. If the user finds their variant(s) of interest, Beacon will point them to the appropriate place to gain access to the data (e.g. the European Genome-Phenome Archive, EGA). @@ -78,87 +78,8 @@ Beacon API SHOULD support cross-origin resource sharing (CORS) and follow [GA4GH - The Automatable Discovery and Access Matrix ([ADAM](https://github.com/ga4gh/ADA-M)) - GA4GH Consent Codes ([GA4GH-CC](https://github.com/ga4gh/ga4gh-consent-policy)) -## Info endpoint - -### Request -##### - URL: `/` -##### - HTTP method: `GET` -##### - Parameters: `None` - -### Response -##### Content-type:`application/json` -##### Payload: `Beacon object` - -**Beacon object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*id* *|Unique identifier of the beacon. Use reverse domain name notation.|string|org.ga4gh.beacon| -|*name* *|Human readable name of the beacon|string|EGA Beacon| -|*apiVersion* *|Version of the API provided by the beacon.|string|v1.0.0| -|*organisation* *|Organisation providing the Beacon|object|Beacon Organisation object (see below)| -|*datasets* *|Datasets served by the beacon. Any beacon should specify at least one dataset.|array|Array of Beacon Dataset objects (see below)| -|description|Description of the beacon.|string|"This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland."| -|version|Version of the Beacon server instance.|string|v0.1| -|welcomeUrl|URL to the welcome page for this beacon (RFC 3986 format).|string|'http://example.org/wiki/Main_Page'| -|alternativeUrl|Alternative URL to the API, e.g. a restricted version of this beacon (RFC 3986 format).|string|'http://example.org/wiki/Main_Page'| -|createDateTime|The time the beacon was created (ISO 8601 format).|string|'2012-07-19 or 2017-01-17T20:33:40Z'| -|updateDateTime|The time the beacon was updated in (ISO 8601 format).|string|'2012-07-19 or 2017-01-17T20:33:40Z'| -|sampleAlleleRequests|Examples of interesting queries, e.g. a few queries demonstrating different responses.|array|Array of BeaconAlleleRequest objects (see _Query endpoint request_)| -|info|'Additional structured metadata, key-value pairs.'|array|-| - -**Beacon Organisation object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*id**|Unique identifier of the organization.|string|-| -|*name**|Name of the organization.|string|-| -|description|Description of the organization.|string|-| -|address|Address of the organization.|string|-| -|welcomeUrl|URL of the website of the organization (RFC 3986 format).|string|-| -|contactUrl|URL with the contact for the beacon operator/maintainer, e.g. link to a contact form (RFC 3986 format) or an email (RFC 2368 format).|string|-| -|logoUrl|URL to the logo (PNG/JPG/SVG format) of the organization (RFC 3986 format).|string|-| -|info|Additional structured metadata, key-value pairs.|string|-| - -**Beacon Dataset object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*id**|Unique identifier of the dataset.|string|-| -|*name**|Name of the dataset.|string|-| -|*assemblyId**|Assembly identifier|string|`'GRCh38'`| -|*createDateTime**|The time the dataset was created (ISO 8601 format).|string|`'2012-07-29 or 2017-01-17T20:33:40Z'`| -|*updateDateTime**|The time the dataset was updated in (ISO 8601 format).|string|`'2012-07-19 or 2017-01-17T20:33:40Z'`| -|description|Description of the dataset.|string|-| -|version|Version of the dataset.|string|-| -|variantCount|Total number of variants in the dataset.|integer|`230453`| -|callCount|Total number of calls in the dataset.|integer|`213454`| -|sampleCount|Total number of samples in the dataset.|integer|`13`| -|externalUrl|URL to an external system providing more dataset information (RFC 3986 format).|string|-| -|info|Additional structured metadata, key-value pairs.|array|-| -|dataUseConditions|The conditions for the use of the dataset|object|Data Use Conditions object (see below)| - -**Data Use Conditions object** - - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*consentCodeDataUse**|The consent code for the use of data.|object|See [GA4GH-CC](https://raw.githubusercontent.com/ga4gh/ga4gh-consent-policy/806ea53cffacb2055c3639f0fc9783f0dcd8cb02/consent_code.yaml#/components/schemas/ConsentCodeDataUse)| -|*adamDataUse**|The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. |object|Adam Data Use Object (see below)| - -**Adam Data Use object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|**header***|General description of what the data is.|object|See [ADA-M](https://raw.githubusercontent.com/ga4gh/ADA-M/b16a72f9987ae20f433e97d6a3247ecddd8dde23/adam.yaml#/components/schemas/Header)| -|**profile***|Profile of the data.|object|See [ADA-M](https://raw.githubusercontent.com/ga4gh/ADA-M/b16a72f9987ae20f433e97d6a3247ecddd8dde23/adam.yaml#/components/schemas/Profile)| -|**terms***|Terms related to the use of the data.|object|See [ADA-M](https://raw.githubusercontent.com/ga4gh/ADA-M/b16a72f9987ae20f433e97d6a3247ecddd8dde23/adam.yaml#/components/schemas/Terms)| -|**metaConditions***|Special conditions.|object|See [ADA-M](https://raw.githubusercontent.com/ga4gh/ADA-M/b16a72f9987ae20f433e97d6a3247ecddd8dde23/adam.yaml#/components/schemas/MetaConditions)| - - - - -### Examples + +### Example Requests and Responses An example `GET` request and response to the info endpoint: > GET / HTTP/1.1 @@ -174,140 +95,83 @@ An example `GET` request and response to the info endpoint: < Date: Fri, 08 Jun 2018 12:07:36 GMT < { + "id": "ega-beacon", + "name": "EGA Beacon", + "apiVersion": "1.1.0", + "organization": { + "id": "EGA", + "name": "European Genome-Phenome Archive (EGA)", + "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", + "address": "", + "welcomeUrl": "https://ega-archive.org/", + "contactUrl": "mailto:beacon.ega@crg.eu", + "logoUrl": "https://ega-archive.org/images/logo.png" + }, + "description": "This Beacon is based on the GA4GH Beacon API 0.4", + "version": "v1.0.0", + "welcomeUrl": "https://ega-archive.org/beacon_web/", "alternativeUrl": "https://ega-archive.org/beacon_web/", - "apiVersion": "0.4", "createDateTime": "2015-06-15T00:00.000Z", - "dataset": [ + "datasets": [ { - "assemblyId": "grch37", - "callCount": 74, - "description": "This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland.", "id": "EGAD00000000028", - "info": {}, - "sampleCount": 1, + "name": "Sample Dataset", + "description": "This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland.", + "assemblyId": "GRCh37", + "createDateTime": "2017-01-17T20:33:40Z", + "updateDateTime": "2017-01-17T20:33:40Z", "variantCount": 74, + "callCount": 74, + "sampleCount": 1, + "info": {} } ], - "description": "This Beacon is based on the GA4GH Beacon API 0.4", - "id": "ega-beacon", - "info": { - "size": "60270153" - }, - "name": "EGA Beacon", - "organization": { - "address": "", - "contactUrl": "mailto:beacon.ega@crg.eu", - "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", - "id": "EGA", - "logoUrl": "https://ega-archive.org/images/logo.png", - "name": "European Genome-Phenome Archive (EGA)", - "welcomeUrl": "https://ega-archive.org/" - }, "sampleAlleleRequests": [ { + "referenceName": "17", + "start": 6689, + "referenceBases": "C", "alternateBases": "A", "assemblyId": "GRCh37", - "includeDatasetResponses": false, - "referenceBases": "C", - "referenceName": "17", - "start": 6689 + "includeDatasetResponses": "NONE" }, { + "referenceName": "1", + "start": 14929, + "referenceBases": "A", "alternateBases": "G", "assemblyId": "GRCh37", "datasetIds": [ "EGAD00000000028" ], - "includeDatasetResponses": "ALL", - "referenceBases": "A", - "referenceName": "1", - "start": 14929 + "includeDatasetResponses": "ALL" }, { + "referenceName": "1", + "start": 866510, + "referenceBases": "C", "alternateBases": "CCCCT", "assemblyId": "GRCh37", "datasetIds": [ "EGAD00001000740", "EGAD00001000741" ], - "includeDatasetResponses": "HIT", - "referenceBases": "C", - "referenceName": "1", - "start": 866510 + "includeDatasetResponses": "HIT" } ], - "version": "v04", - "welcomeUrl": "https://ega-archive.org/beacon_web/" + "info": { + "size": "60270153" + } } * Closing connection 0 -## Query endpoint - - -### Request -##### - URL: `/query` -##### - HTTP method: `GET`, `POST` -##### - Content-Type: `application/x-www-form-urlencoded`(POST) -##### - Parameters: `BeaconAlleleRequest` - -**BeaconAlleleRequest object** - -|Parameter (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*referenceName**|Reference name (chromosome). Accepting values 1-22, X, Y so follows Ensembl chromosome naming convention.|string|`'1'`| -|*referenceBases**|Reference bases for this variant (starting from `start`). Accepted values: [ACGTN]*. N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. For example a sequence where the first and last bases are known, but the middle portion can exhibit countless variations of [ACGT], or the bases are unknown: ANNT the Ns can take take any form of [ACGT], which makes both ACCT and ATGT (or any other combination) viable sequences.
See the REF field in [VCF 4.2 specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf).|string|`'G'`| -|*assemblyId* *|Assembly identifier|string|`'GRCh38'`| -|start~|Precise start coordinate position, allele locus (0-based, inclusive).

* `start` only:
- for single positions, e.g. the start of a specified sequence alteration where the size is given through the specified `alternateBases`
- typical use are queries for SNV and small InDels
- the use of `start` without an `end` parameter requires the use of `referenceBases`
* `start` and `end`:
- special use case for exactly determined structural changes |integer|`345233`| -|startMin~|Minimum start coordinate
* `startMin` + `startMax` + `endMin` + `endMax`:
- for querying imprecise positions (e.g. identifying all structural variants starting anywhere between `startMin` <-> `startMax`, and ending anywhere between `endMin` <-> `endMax`
- single or double sided precise matches can be achieved by setting `startMin` = `startMax` OR `endMin` = `endMax`

For more information on range queries, see: [Beacon-Queries](https://github.com/ga4gh-beacon/specification/wiki/Beacon-Queries#range-queries-and-structural-variants)|integer|`23433`| -|startMax|Maximum start coordinate. See `startMin`.|integer|`23450`| -|end|Precise end coordinate (0-based, exclusive). See `start`.|integer|`455635`| -|endMin|Minimum end coordinate. See `startMin`.|integer|`23500`| -|endMax|Maximum end coordinate. See `startMin`.|integer|`23520`| -|alternateBases~|The bases that appear instead of the reference bases. Accepted values: [ACGTN]*. N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. For example a sequence where the first and last bases are known, but the middle portion can exhibit countless variations of [ACGT], or the bases are unknown: ANNT the Ns can take take any form of [ACGT], which makes both ACCT and ATGT (or any other combination) viable sequences.

Symbolic ALT alleles (DEL, INS, DUP, INV, CNV, DUP:TANDEM, DEL:ME, INS:ME) will be represented in `variantType`.

See the ALT field in [VCF 4.2 specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf)

*Either `alternateBases` OR `variantType` is REQUIRED*|string|`'A'`, `'AGATAC'`| -|variantType~|The `variantType` is used to denote e.g. structural variants.

*Either `alternateBases` OR `variantType` is REQUIRED*|string|`'INS'`, `'DUP'`, `'DEL'`, `'INV'`| -|datasetIds|Identifiers of datasets, as defined in `BeaconDataset`. In case `assemblyId` doesn't match requested dataset(s) error will be raised (`400 Bad request`). If this field is not specified, all datasets should be queried.|array|`['dataset1', 'dataset2']`| -|includeDatasetResponses|Indicator of whether responses for individual datasets (`datasetAlleleResponses`) should be included in the response (`BeaconAlleleResponse`) to this request or not. If null (not specified), the default value of NONE is assumed.

Accepted values : ['ALL', 'HIT', 'MISS', 'NONE']|string|`'ALL'`| - - -### Response -##### Content-type:`application/json` -##### Payload: `Beacon Allele Response object` - -**Beacon Allele Response object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|*beaconId**|Identifier of the beacon, as defined in `Beacon`.|string|-| -|apiVersion|Version of the API. If specified, the value must match `apiVersion` in Beacon|string|-| -|exists|Indicator of whether the given allele was observed in any of the datasets queried. This should be non-null, unless there was an error, in which case `error` has to be non-null.|boolean|`TRUE`| -|alleleRequest|The request that is sent to the Beacon.|object|BeaconAlleleRequest Object (see above _Query endpoint request_)| -|datasetAlleleResponses|The response that the user receives from the Beacon|object|BeaconDatasetAlleleResponse Object (see below)| -|error|The error message and the appropriate HTTP status code|object|See section _Errors_ | - -**Beacon Dataset Allele Response object** - -|Properties (* mandatory, ~ one of these is mandatory)|Description|Type|Example| -|---|---|:---:|---| -|**datasetId***|Unique identifier of the dataset.|string|-| -|exists|Indicator of whether the given allele was observed in the dataset. This should be non-null, unless there was an error, in which case `error` has to be non-null.|boolean|`TRUE`| -|error|The error message and the appropriate HTTP status code|object|See section _Errors_| -|frequency|Frequency of this allele in the dataset. Between 0 and 1, inclusive.|float|`0.07`| -|variantCount|Number of variants matching the allele request in the dataset.|integer|`2`| -|callCount|Number of calls matching the allele request in the dataset.|integer|`3`| -|sampleCount|Number of samples matching the allele request in the dataset|integer|`1`| -|note|Additional note or description of the response.|string|-| -|externalUrl|URL to an external system, such as a secured beacon or a system providing more information about a given allele (RFC 3986 format).|string|-| -|info|Additional structured metadata, key-value pairs.|array|-| - - -#### Examples Example of how to use the GET method in the `/query` endpoint: - curl -v 'https://localhost:5000/query?referenceName=1&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL' + curl -v 'https://localhost:5000/query?referenceName=1&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL' ###### - > GET /query?referenceName=1&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL HTTP/1.1 + > GET /query?referenceName=1&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL HTTP/1.1 > Host: localhost:5000 > User-Agent: curl/7.54.0 > Accept: */* @@ -320,25 +184,36 @@ Example of how to use the GET method in the `/query` endpoint: < Date: Mon, 11 Jun 2018 07:29:26 GMT < { - "beaconId": "ega-beacon", - "apiVersion": "0.4", - "exists": true, - "error": null, - "alleleRequest": { - "referenceName": "1", - "start": 0, - "startMin": 28000000, - "startMax": 29000000, - "end": 0, - "endMin": 28000000, - "endMax": 29000000, - "referenceBases": "A", - "alternateBases": "T", - "assemblyId": "GRCh37", - "datasetIds": [ - "EGAD00000000028" - ], - "includeDatasetResponses": "ALL" + "id": "ega-beacon", + "name": "EGA Beacon", + "apiVersion": "1.1.0", + "organization": { + "id": "EGA", + "name": "European Genome-Phenome Archive (EGA)", + "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", + "address": "", + "welcomeUrl": "https://ega-archive.org/", + "contactUrl": "mailto:beacon.ega@crg.eu", + "logoUrl": "https://ega-archive.org/images/logo.png" + }, + "description": "This Beacon is based on the GA4GH Beacon API 0.4", + "version": "v1.0.0", + "welcomeUrl": "https://ega-archive.org/beacon_web/", + "alternativeUrl": "https://ega-archive.org/beacon_web/", + "createDateTime": "2015-06-15T00:00.000Z", + "alleleRequest": { + "referenceName": "1", + "startMin": 28000000, + "startMax": 29000000, + "endMin": 28000000, + "endMax": 29000000, + "referenceBases": "A", + "alternateBases": "T", + "assemblyId": "GRCh37", + "datasetIds": [ + "EGAD00000000028" + ], + "includeDatasetResponses": "ALL" }, "datasetAlleleResponses": [ { @@ -351,8 +226,27 @@ Example of how to use the GET method in the `/query` endpoint: "note": "This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland.", "externalUrl": null, "info": {}, - "error": null + "datasetHandover": [ + { + "handoverType": { + "id": "EFO:0004157", + "label": "BAM format" + }, + "note": "This handover link provides access to a summarized VCF. To access the VCF containing the details for each sample filling an application is required. See Beacon contact information details.", + "url": "https://api.mygenomeservice.org/handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/" + } + ] } + ], + "beaconHandover": [ + { + "handoverType": { + "id": "EFO:0004157", + "label": "BAM format" + }, + "note": "This handover link provides access to a summarized VCF. To access the VCF containing the details for each sample filling an application is required. See Beacon contact information details.", + "url": "https://api.mygenomeservice.org/handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/" + } ] } * Closing connection 0 @@ -379,18 +273,26 @@ Example of how to use the POST method in the "/query" path: < Date: Mon, 11 Jun 2018 07:15:48 GMT < { - "beaconId": "ega-beacon", - "apiVersion": "0.4", - "exists": true, - "error": null, + "id": "ega-beacon", + "name": "EGA Beacon", + "apiVersion": "1.1.0", + "organization": { + "id": "EGA", + "name": "European Genome-Phenome Archive (EGA)", + "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", + "address": "", + "welcomeUrl": "https://ega-archive.org/", + "contactUrl": "mailto:beacon.ega@crg.eu", + "logoUrl": "https://ega-archive.org/images/logo.png" + }, + "description": "This Beacon is based on the GA4GH Beacon API 0.4", + "version": "v1.0.0", + "welcomeUrl": "https://ega-archive.org/beacon_web/", + "alternativeUrl": "https://ega-archive.org/beacon_web/", + "createDateTime": "2015-06-15T00:00.000Z", "alleleRequest": { "referenceName": "1", "start": 14929, - "startMin": 0, - "startMax": 0, - "end": 0, - "endMin": 0, - "endMax": 0, "referenceBases": "A", "alternateBases": "G", "assemblyId": "GRCh37", @@ -410,13 +312,32 @@ Example of how to use the POST method in the "/query" path: "note": "This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland.", "externalUrl": null, "info": {}, - "error": null + "datasetHandover": [ + { + "handoverType": { + "id": "EFO:0004157", + "label": "BAM format" + }, + "note": "This handover link provides access to a summarized VCF. To access the VCF containing the details for each sample filling an application is required. See Beacon contact information details.", + "url": "https://api.mygenomeservice.org/handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/" + } + ] } + ], + "beaconHandover": [ + { + "handoverType": { + "id": "EFO:0004157", + "label": "BAM format" + }, + "note": "This handover link provides access to a summarized VCF. To access the VCF containing the details for each sample filling an application is required. See Beacon contact information details.", + "url": "https://api.mygenomeservice.org/handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/" + } ] } * Closing connection 0 -`curl -v 'https://localhost:5000/query?&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL'` +`curl -v 'https://localhost:5000/query?startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL'` ``` @@ -436,33 +357,51 @@ Example of how to use the POST method in the "/query" path: < Date: Fri, 06 Jul 2018 09:15:39 GMT < { - "message": { - "beaconId": "ega-beacon", - "apiVersion": "0.4", - "exists": null, - "error": { - "errorCode": 400, - "errorMessage": "Missing mandatory parameter referenceName" - }, - "allelRequest": { - "referenceName": "0", - "start": 0, - "startMin": 28000000, - "startMax": 29000000, - "end": 0, - "endMin": 28000000, - "endMax": 29000000, - "referenceBases": "A", - "alternateBases": "T", - "variantType": "0", - "assemblyId": "GRCh37", - "datasetIds": [ - "EGAD00000000028" - ], - "includeDatasetResponses": "ALL" + "id": "ega-beacon", + "name": "EGA Beacon", + "apiVersion": "1.1.0", + "organization": { + "id": "EGA", + "name": "European Genome-Phenome Archive (EGA)", + "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.", + "address": "", + "welcomeUrl": "https://ega-archive.org/", + "contactUrl": "mailto:beacon.ega@crg.eu", + "logoUrl": "https://ega-archive.org/images/logo.png" + }, + "description": "This Beacon is based on the GA4GH Beacon API 0.4", + "version": "v1.0.0", + "welcomeUrl": "https://ega-archive.org/beacon_web/", + "alternativeUrl": "https://ega-archive.org/beacon_web/", + "createDateTime": "2015-06-15T00:00.000Z", + "error": { + "errorCode": 400, + "errorMessage": "Missing mandatory parameter referenceName" + }, + "allelRequest": { + "startMin": 28000000, + "startMax": 29000000, + "endMin": 28000000, + "endMax": 29000000, + "referenceBases": "A", + "alternateBases": "T", + "assemblyId": "GRCh37", + "datasetIds": [ + "EGAD00000000028" + ], + "includeDatasetResponses": "ALL" + }, + "datasetAlleleResponses": [], + "beaconHandover": [ + { + "handoverType": { + "id": "EFO:0004157", + "label": "BAM format" }, - "datasetAlleleResponses": [] - } + "note": "This handover link provides access to a summarized VCF. To access the VCF containing the details for each sample filling an application is required. See Beacon contact information details.", + "url": "https://api.mygenomeservice.org/handover/9dcc48d7-fc88-11e8-9110-b0c592dbf8c0/" + } + ] } * Closing connection 0