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GA4GH API v1.0.0

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The GA4GH API is available at ga4gh.us.lifeomic.com.

Base URLs:

Authentication

Scope Scope Description

Datasets

Search Datasets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/datasets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/datasets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/datasets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/datasets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/datasets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/datasets/search

Gets a list of Dataset matching the search criteria.

POST /datasets/search must accept a JSON version of SearchDatasetsRequest as the post body and will return a JSON version of SearchDatasetsResponse.

Body parameter

{
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body ga4ghSearchDatasetsRequest true none

Example responses

200 Response

{
  "datasets": [
    {
      "id": "string",
      "name": "string",
      "description": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchDatasetsResponse

Get Dataset

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/datasets/{datasetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/datasets/{datasetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/datasets/{datasetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/datasets/{datasetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/datasets/{datasetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/datasets/{datasetId}

Gets a Dataset by ID.

GET /datasets/{datasetId} will return a JSON version of Dataset.

Parameters

Name In Type Required Description
datasetId path string true none
account path string true none

Example responses

200 Response

{
  "id": "string",
  "name": "string",
  "description": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghDataset

HTSGET

Get Reads

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/htsget/reads/{id} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/htsget/reads/{id}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/htsget/reads/{id}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/htsget/reads/{id}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/htsget/reads/{id}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/htsget/reads/{id}

Streaming API Genomics data.

Allows clients to fetch genomic information in the form of BAM files for reads. A client can reduce the amount of data returned by specifying a reference name and location to fetch.

Parameters

Name In Type Required Description
account path string true The LifeOmic Account
id path string true The ID of the Readgroup Set
referenceName query string false The reference sequence name, for example 'chr1', '1', or 'chrX'. If unspecified, all reads (mapped and unmapped) are returned.
start query number false The start position of the range on the reference, 0-based, inclusive.
end query number false The end position of the range on the reference, 0-based exclusive.

Example responses

200 Response

{
  "htsget": {
    "format": "BAM",
    "urls": [
      {
        "url": "string"
      }
    ]
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghHtsgetResponse

Read Sets

Search Read Sets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "datasetId": "string",
  "name": "string",
  "biosampleId": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/readgroupsets/search

Gets a list of ReadGroupSet matching the search criteria.

POST /readgroupsets/search must accept a JSON version of SearchReadGroupSetsRequest as the post body and will return a JSON version of SearchReadGroupSetsResponse . Only readgroups that match an optionally supplied biosampleId will be included in the response.

Body parameter

{
  "datasetId": "string",
  "name": "string",
  "biosampleId": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body ga4ghSearchReadGroupSetsRequest true none

Example responses

200 Response

{
  "readGroupSets": [
    {
      "id": "string",
      "datasetId": "string",
      "name": "string",
      "stats": {
        "alignedReadCount": "string",
        "unalignedReadCount": "string",
        "baseCount": "string"
      },
      "readGroups": [
        {
          "id": "string",
          "datasetId": "string",
          "name": "string",
          "description": "string",
          "sampleName": "string",
          "biosampleId": "string",
          "experiment": {
            "id": "string",
            "name": "string",
            "description": "string",
            "messageCreateTime": "string",
            "messageUpdateTime": "string",
            "runTime": "string",
            "molecule": "string",
            "strategy": "string",
            "selection": "string",
            "library": "string",
            "libraryLayout": "string",
            "instrumentModel": "string",
            "instrumentDataFile": "string",
            "sequencingCenter": "string",
            "platformUnit": "string",
            "attributes": {
              "attr": {
                "property1": {
                  "values": [
                    {}
                  ]
                },
                "property2": {
                  "values": [
                    {}
                  ]
                }
              }
            }
          },
          "predictedSnsertSize": 0,
          "created": "string",
          "updated": "string",
          "stats": {
            "alignedReadCount": "string",
            "unalignedReadCount": "string",
            "baseCount": "string"
          },
          "programs": [
            {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            }
          ],
          "referenceSetId": "string",
          "attributes": {
            "attr": {
              "property1": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              },
              "property2": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              }
            }
          }
        }
      ],
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchReadGroupSetsResponse

Get Read Set

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/{readGroupSetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/{readGroupSetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/{readGroupSetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/{readGroupSetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/readgroupsets/{readGroupSetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/readgroupsets/{readGroupSetId}

Gets a ReadGroupSet by ID.

GET /readgroupsets/{readGroupSetId} will return a JSON version of ReadGroupSet.

Parameters

Name In Type Required Description
readGroupSetId path string true none
account path string true none

Example responses

200 Response

{
  "id": "string",
  "datasetId": "string",
  "name": "string",
  "stats": {
    "alignedReadCount": "string",
    "unalignedReadCount": "string",
    "baseCount": "string"
  },
  "readGroups": [
    {
      "id": "string",
      "datasetId": "string",
      "name": "string",
      "description": "string",
      "sampleName": "string",
      "biosampleId": "string",
      "experiment": {
        "id": "string",
        "name": "string",
        "description": "string",
        "messageCreateTime": "string",
        "messageUpdateTime": "string",
        "runTime": "string",
        "molecule": "string",
        "strategy": "string",
        "selection": "string",
        "library": "string",
        "libraryLayout": "string",
        "instrumentModel": "string",
        "instrumentDataFile": "string",
        "sequencingCenter": "string",
        "platformUnit": "string",
        "attributes": {
          "attr": {
            "property1": {
              "values": [
                {
                  "stringValue": "string",
                  "int64Value": "string",
                  "int32Value": 0,
                  "boolValue": true,
                  "doubleValue": 0,
                  "externalIdentifier": {
                    "database": "string",
                    "identifier": "string",
                    "version": "string"
                  },
                  "ontologyTerm": {
                    "term_id": "string",
                    "term": "string"
                  },
                  "experiment": null,
                  "program": {
                    "commandLine": "string",
                    "id": "string",
                    "name": "string",
                    "prevProgramId": "string",
                    "version": "string"
                  },
                  "analysis": {
                    "id": "string",
                    "name": "string",
                    "description": "string",
                    "created": "string",
                    "updated": "string",
                    "type": "string",
                    "software": [],
                    "attributes": null
                  },
                  "nullValue": "NULL_VALUE",
                  "attributes": null,
                  "attributeList": null
                }
              ]
            },
            "property2": {
              "values": [
                {
                  "stringValue": "string",
                  "int64Value": "string",
                  "int32Value": 0,
                  "boolValue": true,
                  "doubleValue": 0,
                  "externalIdentifier": {
                    "database": "string",
                    "identifier": "string",
                    "version": "string"
                  },
                  "ontologyTerm": {
                    "term_id": "string",
                    "term": "string"
                  },
                  "experiment": null,
                  "program": {
                    "commandLine": "string",
                    "id": "string",
                    "name": "string",
                    "prevProgramId": "string",
                    "version": "string"
                  },
                  "analysis": {
                    "id": "string",
                    "name": "string",
                    "description": "string",
                    "created": "string",
                    "updated": "string",
                    "type": "string",
                    "software": [],
                    "attributes": null
                  },
                  "nullValue": "NULL_VALUE",
                  "attributes": null,
                  "attributeList": null
                }
              ]
            }
          }
        }
      },
      "predictedSnsertSize": 0,
      "created": "string",
      "updated": "string",
      "stats": {
        "alignedReadCount": "string",
        "unalignedReadCount": "string",
        "baseCount": "string"
      },
      "programs": [
        {
          "commandLine": "string",
          "id": "string",
          "name": "string",
          "prevProgramId": "string",
          "version": "string"
        }
      ],
      "referenceSetId": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghReadGroupSet

Reference Set

Search References

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/references/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "referenceSetId": "string",
  "md5checksum": "string",
  "accession": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/references/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/references/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/references/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/references/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/references/search

Gets a list of Reference matching the search criteria.

POST /references/search must accept a JSON version of SearchReferencesRequest as the post body and will return a JSON version of SearchReferencesResponse.

Body parameter

{
  "referenceSetId": "string",
  "md5checksum": "string",
  "accession": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
body body ga4ghSearchReferencesRequest true none

Example responses

200 Response

{
  "references": [
    {
      "id": "string",
      "length": "string",
      "md5checksum": "string",
      "name": "string",
      "sourceUri": "string",
      "sourceAccessions": [
        "string"
      ],
      "isDerived": true,
      "sourceDivergence": 0,
      "species": {
        "term_id": "string",
        "term": "string"
      },
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchReferencesResponse

Get Reference

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/references/{referenceId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/references/{referenceId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/references/{referenceId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/references/{referenceId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/references/{referenceId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/references/{referenceId}

Gets a Reference by ID.

GET /references/{referenceId} will return a JSON version of Reference.

Parameters

Name In Type Required Description
referenceId path string true none

Example responses

200 Response

{
  "id": "string",
  "length": "string",
  "md5checksum": "string",
  "name": "string",
  "sourceUri": "string",
  "sourceAccessions": [
    "string"
  ],
  "isDerived": true,
  "sourceDivergence": 0,
  "species": {
    "term_id": "string",
    "term": "string"
  },
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghReference

Search Reference Sets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "md5checksum": "string",
  "accession": "string",
  "assemblyId": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/referencesets/search

Gets a list of ReferenceSet matching the search criteria.

POST /referencesets/search must accept a JSON version of SearchReferenceSetsRequest as the post body and will return a JSON version of SearchReferenceSetsResponse.

Body parameter

{
  "md5checksum": "string",
  "accession": "string",
  "assemblyId": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
body body ga4ghSearchReferenceSetsRequest true none

Example responses

200 Response

{
  "referenceSets": [
    {
      "id": "string",
      "name": "string",
      "md5checksum": "string",
      "species": {
        "term_id": "string",
        "term": "string"
      },
      "description": "string",
      "assemblyId": "string",
      "sourceUri": "string",
      "sourceAccessions": [
        "string"
      ],
      "isDerived": true,
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchReferenceSetsResponse

Reference Sets

Get Reference Set

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/{referenceSetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/{referenceSetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/{referenceSetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/{referenceSetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/referencesets/{referenceSetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/referencesets/{referenceSetId}

Gets a ReferenceSet by ID.

GET /referencesets/{referenceSetId} will return a JSON version of ReferenceSet.

Parameters

Name In Type Required Description
referenceSetId path string true none

Example responses

200 Response

{
  "id": "string",
  "name": "string",
  "md5checksum": "string",
  "species": {
    "term_id": "string",
    "term": "string"
  },
  "description": "string",
  "assemblyId": "string",
  "sourceUri": "string",
  "sourceAccessions": [
    "string"
  ],
  "isDerived": true,
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghReferenceSet

RNA Expression Sets

Search RNA Expression Sets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "datasetId": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/rnaquantificationsets/search

Gets a list of 'RnaQuantificationSet' matching the search criteria.

Body parameter

{
  "datasetId": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
body body ga4ghSearchRnaQuantificationSetsRequest true none

Example responses

200 Response

{
  "rnaQuantificationSets": [
    {
      "id": "string",
      "datasetId": "string",
      "name": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchRnaQuantificationSetsResponse

Get RNA Expression Set

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/{rnaQuantificationSetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/{rnaQuantificationSetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/{rnaQuantificationSetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/{rnaQuantificationSetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/rnaquantificationsets/{rnaQuantificationSetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/rnaquantificationsets/{rnaQuantificationSetId}

Gets a RnaQuantificationSet by ID.

Parameters

Name In Type Required Description
rnaQuantificationSetId path string true none

Example responses

200 Response

{
  "id": "string",
  "datasetId": "string",
  "name": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghRnaQuantificationSet

Variant Sets

Search Call Sets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/callsets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "variantSetId": "string",
  "name": "string",
  "biosampleId": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/callsets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/callsets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/callsets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/callsets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/callsets/search

Gets a list of call sets matching the search criteria.

POST /callsets/search must accept a JSON version of SearchCallSetsRequest as the post body and will return a JSON version of SearchCallSetsResponse.

Body parameter

{
  "variantSetId": "string",
  "name": "string",
  "biosampleId": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body ga4ghSearchCallSetsRequest true none

Example responses

200 Response

{
  "callSets": [
    {
      "id": "string",
      "name": "string",
      "biosampleId": "string",
      "variantSetIds": [
        "string"
      ],
      "created": "string",
      "updated": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchCallSetsResponse

Get Call Set

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/callsets/{callSetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/callsets/{callSetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/callsets/{callSetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/callsets/{callSetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/callsets/{callSetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/callsets/{callSetId}

Gets a CallSet by ID.

GET /callsets/{callSetId} will return a JSON version of CallSet.

Parameters

Name In Type Required Description
callSetId path string true none
account path string true none

Example responses

200 Response

{
  "id": "string",
  "name": "string",
  "biosampleId": "string",
  "variantSetIds": [
    "string"
  ],
  "created": "string",
  "updated": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Responses

Status Meaning Description Schema
200 OK none ga4ghCallSet

Search Variants

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/variants/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "variantSetId": "string",
  "callSetIds": [
    "string"
  ],
  "referenceName": "string",
  "start": "string",
  "end": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/variants/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/variants/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/variants/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/variants/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/variants/search

Gets a list of Variant matching the search criteria.

POST /variants/search must accept a JSON version of SearchVariantsRequest as the post body and will return a JSON version of SearchVariantsResponse.

Body parameter

{
  "variantSetId": "string",
  "callSetIds": [
    "string"
  ],
  "referenceName": "string",
  "start": "string",
  "end": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body ga4ghSearchVariantsRequest true none

Example responses

200 Response

{
  "variants": [
    {
      "id": "string",
      "variantSetId": "string",
      "names": [
        "string"
      ],
      "created": "string",
      "updated": "string",
      "referenceName": "string",
      "start": "string",
      "end": "string",
      "referenceBases": "string",
      "alternateBases": [
        "string"
      ],
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      },
      "calls": [
        {
          "callCetName": "string",
          "callSetId": "string",
          "genotype": {
            "values": [
              {
                "nullValue": "NULL_VALUE",
                "numberValue": 0,
                "stringValue": "string",
                "boolValue": true,
                "structValue": {
                  "fields": {}
                },
                "listValue": null
              }
            ]
          },
          "phaseset": "string",
          "genotypeLikelihood": [
            0
          ],
          "attributes": {
            "attr": {
              "property1": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              },
              "property2": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              }
            }
          }
        }
      ],
      "variantType": "string",
      "svlen": "string",
      "cipos": [
        0
      ],
      "ciend": [
        0
      ],
      "filtersApplied": true,
      "filtersPassed": true,
      "filtersFailed": [
        "string"
      ]
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchVariantsResponse

Get Variant

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/variants/{variantId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/variants/{variantId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/variants/{variantId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/variants/{variantId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/variants/{variantId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/variants/{variantId}

Gets a Variant by ID.

GET /variants/{variantId} will return a JSON version of Variant.

Parameters

Name In Type Required Description
variantId path string true none
account path string true none

Example responses

200 Response

{
  "id": "string",
  "variantSetId": "string",
  "names": [
    "string"
  ],
  "created": "string",
  "updated": "string",
  "referenceName": "string",
  "start": "string",
  "end": "string",
  "referenceBases": "string",
  "alternateBases": [
    "string"
  ],
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  },
  "calls": [
    {
      "callCetName": "string",
      "callSetId": "string",
      "genotype": {
        "values": [
          {
            "nullValue": "NULL_VALUE",
            "numberValue": 0,
            "stringValue": "string",
            "boolValue": true,
            "structValue": {
              "fields": {}
            },
            "listValue": null
          }
        ]
      },
      "phaseset": "string",
      "genotypeLikelihood": [
        0
      ],
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "variantType": "string",
  "svlen": "string",
  "cipos": [
    0
  ],
  "ciend": [
    0
  ],
  "filtersApplied": true,
  "filtersPassed": true,
  "filtersFailed": [
    "string"
  ]
}

Responses

Status Meaning Description Schema
200 OK none ga4ghVariant

Search Variant Sets

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/search \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "dataset_id": "string",
  "pageSize": 0,
  "pageToken": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/search',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/search', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/search");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/search", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/variantsets/search

Gets a list of VariantSet matching the search criteria.

POST /variantsets/search must accept a JSON version of SearchVariantSetsRequest as the post body and will return a JSON version of SearchVariantSetsResponse.

Body parameter

{
  "dataset_id": "string",
  "pageSize": 0,
  "pageToken": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body ga4ghSearchVariantSetsRequest true none

Example responses

200 Response

{
  "variantSets": [
    {
      "id": "string",
      "name": "string",
      "datasetId": "string",
      "referenceSetId": "string",
      "metadata": [
        {
          "key": "string",
          "value": "string",
          "id": "string",
          "type": "string",
          "number": "string",
          "description": "string",
          "attributes": {
            "attr": {
              "property1": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              },
              "property2": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              }
            }
          }
        }
      ]
    }
  ],
  "nextPageToken": "string"
}

Responses

Status Meaning Description Schema
200 OK none ga4ghSearchVariantSetsResponse

Create Genomic Set

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/genomicsets \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/genomicsets',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/genomicsets', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/genomicsets");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/genomicsets", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/genomicsets

Create a variant and readgroup set

Create a variant and readgroup set.

Body parameter

{}

Parameters

Name In Type Required Description
account path string true none
body body GenomicSet true none

Example responses

200 Response

{}

Responses

Status Meaning Description Schema
200 OK none GenomicSet

Get Variant Set

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/{variantSetId} \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/{variantSetId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/{variantSetId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/{variantSetId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/{account}/v1/variantsets/{variantSetId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /{account}/v1/variantsets/{variantSetId}

Gets a VariantSet by ID.

GET /variantsets/{variantSetId} will return a JSON version of VariantSet.

Parameters

Name In Type Required Description
variantSetId path string true none
account path string true none

Example responses

200 Response

{
  "id": "string",
  "name": "string",
  "datasetId": "string",
  "referenceSetId": "string",
  "metadata": [
    {
      "key": "string",
      "value": "string",
      "id": "string",
      "type": "string",
      "number": "string",
      "description": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ]
}

Responses

Status Meaning Description Schema
200 OK none ga4ghVariantSet

Copynumber Sets

Create Copynumber Set

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/copynumbersets \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "sequenceId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/copynumbersets',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/copynumbersets', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/copynumbersets");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/copynumbersets", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/copynumbersets

Create a copy number set.

Create a copy number set

Body parameter

{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "sequenceId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body CopyNumberSet true none

Example responses

200 Response

{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "sequenceId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}

Responses

Status Meaning Description Schema
200 OK none CopyNumberSet

Structural Variant Sets

Create Structural Variant Set

Code samples

# You can also use wget
curl -X POST https://ga4gh.us.lifeomic.com/{account}/v1/fusionsets \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');
const inputBody = '{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "sequenceId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}';
const headers = {
  'Content-Type':'application/json',
  'Accept':'application/json',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/{account}/v1/fusionsets',
{
  method: 'POST',
  body: inputBody,
  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Content-Type': 'application/json',
  'Accept': 'application/json',
  'Authorization': 'API_KEY'
}

r = requests.post('https://ga4gh.us.lifeomic.com/{account}/v1/fusionsets', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/{account}/v1/fusionsets");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("POST");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Content-Type": []string{"application/json"},
        "Accept": []string{"application/json"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("POST", "https://ga4gh.us.lifeomic.com/{account}/v1/fusionsets", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

POST /{account}/v1/fusionsets

Create a structural variant set.

Create a structural variant set

Body parameter

{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "sequenceId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}

Parameters

Name In Type Required Description
account path string true none
body body FusionSet true none

Example responses

200 Response

{
  "datasetId": "string",
  "fileId": "string",
  "reportFileId": "string",
  "name": "string",
  "patientId": "string",
  "indexedDate": "string",
  "performerId": "string",
  "sequenceId": "string",
  "referenceSetId": "GRCh37",
  "sequenceType": "germline",
  "testId": "string",
  "testType": "string",
  "useExistingSequence": true,
  "sourceFileId": "string",
  "bodySite": "string",
  "bodySiteSystem": "string",
  "bodySiteDisplay": "string"
}

Responses

Status Meaning Description Schema
200 OK none FusionSet

DRS

Get DRS Object Access

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}/access/https \
  -H 'Accept: application/json' \
  -H 'LifeOmic-Account: string' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'LifeOmic-Account':'string',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}/access/https',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'LifeOmic-Account': 'string',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}/access/https', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}/access/https");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "LifeOmic-Account": []string{"string"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}/access/https", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /ga4gh/drs/v1/objects/{objectId}/access/https

Get information about how to access a DRS object

Get information about how to access a DRS object

Parameters

Name In Type Required Description
LifeOmic-Account header string true The LifeOmic account to access.
objectId path string true The object id.

Example responses

200 Response

{
  "url": "string"
}

Responses

Status Meaning Description Schema
200 OK none DRSObjectAccess

Get DRS Object

Code samples

# You can also use wget
curl -X GET https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId} \
  -H 'Accept: application/json' \
  -H 'LifeOmic-Account: string' \
  -H 'Authorization: API_KEY'

const fetch = require('node-fetch');

const headers = {
  'Accept':'application/json',
  'LifeOmic-Account':'string',
  'Authorization':'API_KEY'

};

fetch('https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}',
{
  method: 'GET',

  headers: headers
})
.then(function(res) {
    return res.json();
}).then(function(body) {
    console.log(body);
});

import requests
headers = {
  'Accept': 'application/json',
  'LifeOmic-Account': 'string',
  'Authorization': 'API_KEY'
}

r = requests.get('https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}', params={

}, headers = headers)

print r.json()

URL obj = new URL("https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}");
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
con.setRequestMethod("GET");
int responseCode = con.getResponseCode();
BufferedReader in = new BufferedReader(
    new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
    response.append(inputLine);
}
in.close();
System.out.println(response.toString());

package main

import (
       "bytes"
       "net/http"
)

func main() {

    headers := map[string][]string{
        "Accept": []string{"application/json"},
        "LifeOmic-Account": []string{"string"},
        "Authorization": []string{"API_KEY"},

    }

    data := bytes.NewBuffer([]byte{jsonReq})
    req, err := http.NewRequest("GET", "https://ga4gh.us.lifeomic.com/ga4gh/drs/v1/objects/{objectId}", data)
    req.Header = headers

    client := &http.Client{}
    resp, err := client.Do(req)
    // ...
}

GET /ga4gh/drs/v1/objects/{objectId}

Get information about a DRS object

Get information about a DRS object

Parameters

Name In Type Required Description
LifeOmic-Account header string true The LifeOmic account to access.
objectId path string true The object id.

Example responses

200 Response

{
  "id": "string",
  "created_time": "string",
  "updated_time": "string",
  "version": "string",
  "mime_type": "string",
  "name": "string",
  "self_uri": "string",
  "size": "string",
  "checksums": [
    {
      "checksum": "string",
      "type": "string"
    }
  ],
  "access_methods": [
    {
      "access_id": "string",
      "type": "string"
    }
  ]
}

Responses

Status Meaning Description Schema
200 OK none DRSObject

Schemas

ga4ghAnalysis

{
  "id": "string",
  "name": "string",
  "description": "string",
  "created": "string",
  "updated": "string",
  "type": "string",
  "software": [
    "string"
  ],
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": null,
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": null,
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used.

Properties

Name Type Required Restrictions Description
id string false none Formats of id
name string false none none
description string false none none
created string false none The time at which this record was created, in ISO 8601 format.
updated string false none The time at which this record was last updated, in ISO 8601 format.
type string false none The type of analysis.
software [string] false none The software run to generate this analysis.
attributes ga4ghAttributes false none none

ga4ghAttributeValue

{
  "stringValue": "string",
  "int64Value": "string",
  "int32Value": 0,
  "boolValue": true,
  "doubleValue": 0,
  "externalIdentifier": {
    "database": "string",
    "identifier": "string",
    "version": "string"
  },
  "ontologyTerm": {
    "term_id": "string",
    "term": "string"
  },
  "experiment": {
    "id": "string",
    "name": "string",
    "description": "string",
    "messageCreateTime": "string",
    "messageUpdateTime": "string",
    "runTime": "string",
    "molecule": "string",
    "strategy": "string",
    "selection": "string",
    "library": "string",
    "libraryLayout": "string",
    "instrumentModel": "string",
    "instrumentDataFile": "string",
    "sequencingCenter": "string",
    "platformUnit": "string",
    "attributes": {
      "attr": {
        "property1": {
          "values": [
            null
          ]
        },
        "property2": {
          "values": [
            null
          ]
        }
      }
    }
  },
  "program": {
    "commandLine": "string",
    "id": "string",
    "name": "string",
    "prevProgramId": "string",
    "version": "string"
  },
  "analysis": {
    "id": "string",
    "name": "string",
    "description": "string",
    "created": "string",
    "updated": "string",
    "type": "string",
    "software": [
      "string"
    ],
    "attributes": {
      "attr": {
        "property1": {
          "values": [
            null
          ]
        },
        "property2": {
          "values": [
            null
          ]
        }
      }
    }
  },
  "nullValue": "NULL_VALUE",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          null
        ]
      },
      "property2": {
        "values": [
          null
        ]
      }
    }
  },
  "attributeList": {
    "values": [
      null
    ]
  }
}

Type defining a collection of attributes associated with various protocol records. Each attribute is a name that maps to an array of one or more values. Values are chosen from both internal protobuf types and GA4GH. Values should be split into array elements instead of using a separator syntax that needs to parsed.

Properties

Name Type Required Restrictions Description
stringValue string false none none
int64Value string(int64) false none none
int32Value integer(int32) false none none
boolValue boolean(boolean) false none none
doubleValue number(double) false none none
externalIdentifier ga4ghExternalIdentifier false none none
ontologyTerm ga4ghOntologyTerm false none none
experiment ga4ghExperiment false none An experimental preparation of a sample.
program ga4ghProgram false none A Program describes software used in data processing or analysis.
analysis ga4ghAnalysis false none An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used.
nullValue ga4ghNullValue false none - NULL_VALUE: Null value.
attributes ga4ghAttributes false none none
attributeList ga4ghAttributeValueList false none none

ga4ghAttributeValueList

{
  "values": [
    {
      "stringValue": "string",
      "int64Value": "string",
      "int32Value": 0,
      "boolValue": true,
      "doubleValue": 0,
      "externalIdentifier": {
        "database": "string",
        "identifier": "string",
        "version": "string"
      },
      "ontologyTerm": {
        "term_id": "string",
        "term": "string"
      },
      "experiment": {
        "id": "string",
        "name": "string",
        "description": "string",
        "messageCreateTime": "string",
        "messageUpdateTime": "string",
        "runTime": "string",
        "molecule": "string",
        "strategy": "string",
        "selection": "string",
        "library": "string",
        "libraryLayout": "string",
        "instrumentModel": "string",
        "instrumentDataFile": "string",
        "sequencingCenter": "string",
        "platformUnit": "string",
        "attributes": {
          "attr": {}
        }
      },
      "program": {
        "commandLine": "string",
        "id": "string",
        "name": "string",
        "prevProgramId": "string",
        "version": "string"
      },
      "analysis": {
        "id": "string",
        "name": "string",
        "description": "string",
        "created": "string",
        "updated": "string",
        "type": "string",
        "software": [
          "string"
        ],
        "attributes": {
          "attr": {}
        }
      },
      "nullValue": "NULL_VALUE",
      "attributes": {
        "attr": {}
      },
      "attributeList": null
    }
  ]
}

Properties

Name Type Required Restrictions Description
values [ga4ghAttributeValue] false none [Type defining a collection of attributes associated with various protocol records. Each attribute is a name that maps to an array of one or more values. Values are chosen from both internal protobuf types and GA4GH. Values should be split into array elements instead of using a separator syntax that needs to parsed.]

ga4ghAttributes

{
  "attr": {
    "property1": {
      "values": [
        {
          "stringValue": "string",
          "int64Value": "string",
          "int32Value": 0,
          "boolValue": true,
          "doubleValue": 0,
          "externalIdentifier": {
            "database": "string",
            "identifier": "string",
            "version": "string"
          },
          "ontologyTerm": {
            "term_id": "string",
            "term": "string"
          },
          "experiment": {
            "id": "string",
            "name": "string",
            "description": "string",
            "messageCreateTime": "string",
            "messageUpdateTime": "string",
            "runTime": "string",
            "molecule": "string",
            "strategy": "string",
            "selection": "string",
            "library": "string",
            "libraryLayout": "string",
            "instrumentModel": "string",
            "instrumentDataFile": "string",
            "sequencingCenter": "string",
            "platformUnit": "string",
            "attributes": null
          },
          "program": {
            "commandLine": "string",
            "id": "string",
            "name": "string",
            "prevProgramId": "string",
            "version": "string"
          },
          "analysis": {
            "id": "string",
            "name": "string",
            "description": "string",
            "created": "string",
            "updated": "string",
            "type": "string",
            "software": [
              "string"
            ],
            "attributes": null
          },
          "nullValue": "NULL_VALUE",
          "attributes": null,
          "attributeList": null
        }
      ]
    },
    "property2": {
      "values": [
        {
          "stringValue": "string",
          "int64Value": "string",
          "int32Value": 0,
          "boolValue": true,
          "doubleValue": 0,
          "externalIdentifier": {
            "database": "string",
            "identifier": "string",
            "version": "string"
          },
          "ontologyTerm": {
            "term_id": "string",
            "term": "string"
          },
          "experiment": {
            "id": "string",
            "name": "string",
            "description": "string",
            "messageCreateTime": "string",
            "messageUpdateTime": "string",
            "runTime": "string",
            "molecule": "string",
            "strategy": "string",
            "selection": "string",
            "library": "string",
            "libraryLayout": "string",
            "instrumentModel": "string",
            "instrumentDataFile": "string",
            "sequencingCenter": "string",
            "platformUnit": "string",
            "attributes": null
          },
          "program": {
            "commandLine": "string",
            "id": "string",
            "name": "string",
            "prevProgramId": "string",
            "version": "string"
          },
          "analysis": {
            "id": "string",
            "name": "string",
            "description": "string",
            "created": "string",
            "updated": "string",
            "type": "string",
            "software": [
              "string"
            ],
            "attributes": null
          },
          "nullValue": "NULL_VALUE",
          "attributes": null,
          "attributeList": null
        }
      ]
    }
  }
}

Properties

Name Type Required Restrictions Description
attr object false none none
ยป additionalProperties ga4ghAttributeValueList false none none

ga4ghDataset

{
  "id": "string",
  "name": "string",
  "description": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

A Dataset is a collection of related data of multiple types. Data providers decide how to group data into datasets. See Project API for a more detailed discussion.

Properties

Name Type Required Restrictions Description
id string false none The dataset's id, locally unique to the server instance.
name string false none The name of the dataset.
description string false none Additional, human-readable information on the dataset.
attributes ga4ghAttributes false none none

ga4ghExperiment

{
  "id": "string",
  "name": "string",
  "description": "string",
  "messageCreateTime": "string",
  "messageUpdateTime": "string",
  "runTime": "string",
  "molecule": "string",
  "strategy": "string",
  "selection": "string",
  "library": "string",
  "libraryLayout": "string",
  "instrumentModel": "string",
  "instrumentDataFile": "string",
  "sequencingCenter": "string",
  "platformUnit": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": null,
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": null,
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

An experimental preparation of a sample.

Properties

Name Type Required Restrictions Description
id string false none none
name string false none The name of the experiment.
description string false none A description of the experiment.
messageCreateTime string false none none
messageUpdateTime string false none none
runTime string false none none
molecule string false none none
strategy string false none none
selection string false none none
library string false none The name of the library used as part of this experiment.
libraryLayout string false none The configuration of sequenced reads. (e.g. Single or Paired).
instrumentModel string false none The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
instrumentDataFile string false none none
sequencingCenter string false none The sequencing center used as part of this experiment.
platformUnit string false none The platform unit used as part of this experiment. This is a flowcell-barcode or slide unique identifier.
attributes ga4ghAttributes false none none

ga4ghExternalIdentifier

{
  "database": "string",
  "identifier": "string",
  "version": "string"
}

Identifier from a public database

Properties

Name Type Required Restrictions Description
database string false none The source of the identifier, e.g. Ensembl.
identifier string false none The ID defined by the external database, e.g. ENST00000000000.
version string false none The version of the object or the database, e.g. 78.

ga4ghNullValue

"NULL_VALUE"

Properties

Name Type Required Restrictions Description
anonymous string false none - NULL_VALUE: Null value.

Enumerated Values

Property Value
anonymous NULL_VALUE

ga4ghOntologyTerm

{
  "term_id": "string",
  "term": "string"
}

An ontology term describing an attribute. (e.g. the phenotype attribute 'polydactyly' from HPO)

Properties

Name Type Required Restrictions Description
term_id string false none Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:id <apidesign_object_ids> in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation.
term string false none Ontology term - the label of the ontology term the termId is pointing to.

ga4ghProgram

{
  "commandLine": "string",
  "id": "string",
  "name": "string",
  "prevProgramId": "string",
  "version": "string"
}

A Program describes software used in data processing or analysis.

Properties

Name Type Required Restrictions Description
commandLine string false none The command line used to run this program.
id string false none The user specified ID of the program.
name string false none The name of the program.
prevProgramId string false none The ID of the program run before this one.
version string false none The version of the program run.

ga4ghSearchDatasetsRequest

{
  "pageSize": 0,
  "pageToken": "string"
}

This request maps to the body of POST /datasets/search as JSON.

Properties

Name Type Required Restrictions Description
pageSize integer(int32) false none Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
pageToken string false none The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of next_page_token from the previous response.

ga4ghSearchDatasetsResponse

{
  "datasets": [
    {
      "id": "string",
      "name": "string",
      "description": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

This is the response from POST /datasets/search expressed as JSON.

Properties

Name Type Required Restrictions Description
datasets [ga4ghDataset] false none The list of datasets.
nextPageToken string false none The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.

CigarUnitOperation

"OPERATION_UNSPECIFIED"

*Describes the different types of CIGAR alignment operations that exist.

Used wherever CIGAR alignments are used.

Properties

Name Type Required Restrictions Description
anonymous string false none Describes the different types of CIGAR alignment operations that exist. Used wherever CIGAR alignments are used. - OPERATION_UNSPECIFIED: The null operation. - ALIGNMENT_MATCH: An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. This operator is equivalent to SAM's M. - INSERT: The insert operator indicates that the read contains evidence of bases being inserted into the reference. This operator is equivalent to SAM's I. - DELETE: The delete operator indicates that the read contains evidence of bases being deleted from the reference. This operator is equivalent to SAM's D. - SKIP: The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. This operator is equivalent to SAM's N. - CLIP_SOFT: The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. This operator is equivalent to SAM's S. Bases that are soft clipped will still be stored in the read. - CLIP_HARD: The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (for example, during error correction or to trim poly-A tails for RNA-seq). This operator is equivalent to SAM's H. - PAD: The pad operator indicates that there is padding in an alignment. This operator is equivalent to SAM's P. - SEQUENCE_MATCH: This operator indicates that this portion of the aligned sequence exactly matches the reference. This operator is equivalent to SAM's =. - SEQUENCE_MISMATCH: This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch. This can indicate a SNP or a read error. This operator is equivalent to SAM's X.

Enumerated Values

Property Value
anonymous OPERATION_UNSPECIFIED
anonymous ALIGNMENT_MATCH
anonymous INSERT
anonymous DELETE
anonymous SKIP
anonymous CLIP_SOFT
anonymous CLIP_HARD
anonymous PAD
anonymous SEQUENCE_MATCH
anonymous SEQUENCE_MISMATCH

ga4ghCigarUnit

{
  "operation": "OPERATION_UNSPECIFIED",
  "operationLength": "string",
  "referenceSequence": "string"
}

A single CIGAR operation.

Properties

Name Type Required Restrictions Description
operation CigarUnitOperation false none Describes the different types of CIGAR alignment operations that exist. Used wherever CIGAR alignments are used. - OPERATION_UNSPECIFIED: The null operation. - ALIGNMENT_MATCH: An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. This operator is equivalent to SAM's M. - INSERT: The insert operator indicates that the read contains evidence of bases being inserted into the reference. This operator is equivalent to SAM's I. - DELETE: The delete operator indicates that the read contains evidence of bases being deleted from the reference. This operator is equivalent to SAM's D. - SKIP: The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. This operator is equivalent to SAM's N. - CLIP_SOFT: The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. This operator is equivalent to SAM's S. Bases that are soft clipped will still be stored in the read. - CLIP_HARD: The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (for example, during error correction or to trim poly-A tails for RNA-seq). This operator is equivalent to SAM's H. - PAD: The pad operator indicates that there is padding in an alignment. This operator is equivalent to SAM's P. - SEQUENCE_MATCH: This operator indicates that this portion of the aligned sequence exactly matches the reference. This operator is equivalent to SAM's =. - SEQUENCE_MISMATCH: This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch. This can indicate a SNP or a read error. This operator is equivalent to SAM's X.
operationLength string(int64) false none The number of genomic bases that the operation runs for. Required.
referenceSequence string false none referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and deletions (DELETE). Filling this field replaces SAM's MD tag. If the relevant information is not available, this field is unset.

ga4ghLinearAlignment

{
  "position": {
    "referenceName": "string",
    "position": "string",
    "strand": "STRAND_UNSPECIFIED"
  },
  "mappingQuality": 0,
  "cigar": [
    {
      "operation": "OPERATION_UNSPECIFIED",
      "operationLength": "string",
      "referenceSequence": "string"
    }
  ]
}

A linear alignment describes the alignment of a read to a Reference, using a position and CIGAR array.

Properties

Name Type Required Restrictions Description
position ga4ghPosition false none A Position is an unoriented base in some Reference. A Position is represented by a Reference name, and a base number on that Reference (0-based).
mappingQuality integer(int32) false none The mapping quality of this alignment, meaning the likelihood that the read maps to this position. Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the nearest integer.
cigar [ga4ghCigarUnit] false none Represents the local alignment of this sequence (alignment matches, indels, etc) versus the reference.

ga4ghPosition

{
  "referenceName": "string",
  "position": "string",
  "strand": "STRAND_UNSPECIFIED"
}

A Position is an unoriented base in some Reference. A Position is represented by a Reference name, and a base number on that Reference (0-based).

Properties

Name Type Required Restrictions Description
referenceName string false none The name of the Reference on which the Position is located.
position string(int64) false none The 0-based offset from the start of the forward strand for that Reference. Genomic positions are non-negative integers less than Reference length.
strand ga4ghStrand false none Indicates the associated DNA strand for some data item. - STRAND_UNSPECIFIED: If no strand data is available. - NEG_STRAND: The negative (-) strand. - POS_STRAND: The postive (+) strand.

ga4ghReadAlignment

{
  "id": "string",
  "readGroupId": "string",
  "fragmentName": "string",
  "improperPlacement": true,
  "duplicateFragment": true,
  "numberReads": 0,
  "fragmentLength": 0,
  "readNumber": 0,
  "failedVendorQualityChecks": true,
  "alignment": {
    "position": {
      "referenceName": "string",
      "position": "string",
      "strand": "STRAND_UNSPECIFIED"
    },
    "mappingQuality": 0,
    "cigar": [
      {
        "operation": "OPERATION_UNSPECIFIED",
        "operationLength": "string",
        "referenceSequence": "string"
      }
    ]
  },
  "secondaryAlignment": true,
  "supplementaryAlignment": true,
  "alignedSequence": "string",
  "alignedQuality": [
    0
  ],
  "nextMatePosition": {
    "referenceName": "string",
    "position": "string",
    "strand": "STRAND_UNSPECIFIED"
  },
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

Each read alignment describes an alignment with additional information about the fragment and the read. A read alignment object is equivalent to line in a SAM file.

Properties

Name Type Required Restrictions Description
id string false none The read alignment ID. This ID is unique within the read group this alignment belongs to. For performance reasons, this field may be omitted by a backend. If provided, its intended use is to make caching and UI display easier for genome browsers and other lightweight clients.
readGroupId string false none none
fragmentName string false none The fragment name. Equivalent to QNAME (query template name) in SAM.
improperPlacement boolean(boolean) false none The orientation and the distance between reads from the fragment are inconsistent with the sequencing protocol (inverse of SAM flag 0x2).
duplicateFragment boolean(boolean) false none The fragment is a PCR or optical duplicate (SAM flag 0x400).
numberReads integer(int32) false none The number of reads in the fragment (extension to SAM flag 0x1).
fragmentLength integer(int32) false none The observed length of the fragment, equivalent to TLEN in SAM.
readNumber integer(int32) false none The read ordinal in the fragment, 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80 and is intended to more cleanly represent multiple reads per fragment.
failedVendorQualityChecks boolean(boolean) false none The read fails platform or vendor quality checks (SAM flag 0x200).
alignment ga4ghLinearAlignment false none A linear alignment describes the alignment of a read to a Reference, using a position and CIGAR array.
secondaryAlignment boolean(boolean) false none Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both secondaryAlignment and supplementaryAlignment are false.
supplementaryAlignment boolean(boolean) false none Whether this alignment is supplementary. Equivalent to SAM flag 0x800. Supplementary alignments are used in the representation of a chimeric alignment. In a chimeric alignment, a read is split into multiple linear alignments that map to different reference contigs. The first linear alignment in the read will be designated as the representative alignment; the remaining linear alignments will be designated as supplementary alignments. These alignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The alignedSequence and alignedQuality fields in the alignment message will only represent the bases for its respective linear alignment.
alignedSequence string false none The bases of the read sequence contained in this alignment record (equivalent to SEQ in SAM). alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.
alignedQuality [integer] false none The quality of the read sequence contained in this alignment message (equivalent to QUAL in SAM). alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.
nextMatePosition ga4ghPosition false none A Position is an unoriented base in some Reference. A Position is represented by a Reference name, and a base number on that Reference (0-based).
attributes ga4ghAttributes false none none

ga4ghReadGroup

{
  "id": "string",
  "datasetId": "string",
  "name": "string",
  "description": "string",
  "sampleName": "string",
  "biosampleId": "string",
  "experiment": {
    "id": "string",
    "name": "string",
    "description": "string",
    "messageCreateTime": "string",
    "messageUpdateTime": "string",
    "runTime": "string",
    "molecule": "string",
    "strategy": "string",
    "selection": "string",
    "library": "string",
    "libraryLayout": "string",
    "instrumentModel": "string",
    "instrumentDataFile": "string",
    "sequencingCenter": "string",
    "platformUnit": "string",
    "attributes": {
      "attr": {
        "property1": {
          "values": [
            {
              "stringValue": "string",
              "int64Value": "string",
              "int32Value": 0,
              "boolValue": true,
              "doubleValue": 0,
              "externalIdentifier": {
                "database": "string",
                "identifier": "string",
                "version": "string"
              },
              "ontologyTerm": {
                "term_id": "string",
                "term": "string"
              },
              "experiment": null,
              "program": {
                "commandLine": "string",
                "id": "string",
                "name": "string",
                "prevProgramId": "string",
                "version": "string"
              },
              "analysis": {
                "id": "string",
                "name": "string",
                "description": "string",
                "created": "string",
                "updated": "string",
                "type": "string",
                "software": [
                  "string"
                ],
                "attributes": null
              },
              "nullValue": "NULL_VALUE",
              "attributes": null,
              "attributeList": null
            }
          ]
        },
        "property2": {
          "values": [
            {
              "stringValue": "string",
              "int64Value": "string",
              "int32Value": 0,
              "boolValue": true,
              "doubleValue": 0,
              "externalIdentifier": {
                "database": "string",
                "identifier": "string",
                "version": "string"
              },
              "ontologyTerm": {
                "term_id": "string",
                "term": "string"
              },
              "experiment": null,
              "program": {
                "commandLine": "string",
                "id": "string",
                "name": "string",
                "prevProgramId": "string",
                "version": "string"
              },
              "analysis": {
                "id": "string",
                "name": "string",
                "description": "string",
                "created": "string",
                "updated": "string",
                "type": "string",
                "software": [
                  "string"
                ],
                "attributes": null
              },
              "nullValue": "NULL_VALUE",
              "attributes": null,
              "attributeList": null
            }
          ]
        }
      }
    }
  },
  "predictedSnsertSize": 0,
  "created": "string",
  "updated": "string",
  "stats": {
    "alignedReadCount": "string",
    "unalignedReadCount": "string",
    "baseCount": "string"
  },
  "programs": [
    {
      "commandLine": "string",
      "id": "string",
      "name": "string",
      "prevProgramId": "string",
      "version": "string"
    }
  ],
  "referenceSetId": "string",
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

A ReadGroup is a set of reads derived from one physical sequencing process.

Properties

Name Type Required Restrictions Description
id string false none The read group ID.
datasetId string false none The ID of the dataset this read group belongs to.
name string false none The read group name.
description string false none The read group description.
sampleName string false none A name for the sample this read group's data were generated from. This field contains an arbitrary string, typically corresponding to the SM tag in a BAM file.
biosampleId string false none The Biosample this read group's data was generated from.
experiment ga4ghExperiment false none An experimental preparation of a sample.
predictedSnsertSize integer(int32) false none The predicted insert size of this read group.
created string(int64) false none The time at which this read group was created in milliseconds from the epoch.
updated string(int64) false none The time at which this read group was last updated in milliseconds from the epoch.
stats ga4ghReadStats false none ReadStats can be used to provide summary statistics about read data.
programs [ga4ghProgram] false none Program can be used to track the provenance of how read data was generated.
referenceSetId string false none The ID of the reference set to which the reads in this read group are aligned. Required if there are any read alignments.
attributes ga4ghAttributes false none none

ga4ghReadGroupSet

{
  "id": "string",
  "datasetId": "string",
  "name": "string",
  "stats": {
    "alignedReadCount": "string",
    "unalignedReadCount": "string",
    "baseCount": "string"
  },
  "readGroups": [
    {
      "id": "string",
      "datasetId": "string",
      "name": "string",
      "description": "string",
      "sampleName": "string",
      "biosampleId": "string",
      "experiment": {
        "id": "string",
        "name": "string",
        "description": "string",
        "messageCreateTime": "string",
        "messageUpdateTime": "string",
        "runTime": "string",
        "molecule": "string",
        "strategy": "string",
        "selection": "string",
        "library": "string",
        "libraryLayout": "string",
        "instrumentModel": "string",
        "instrumentDataFile": "string",
        "sequencingCenter": "string",
        "platformUnit": "string",
        "attributes": {
          "attr": {
            "property1": {
              "values": [
                {
                  "stringValue": "string",
                  "int64Value": "string",
                  "int32Value": 0,
                  "boolValue": true,
                  "doubleValue": 0,
                  "externalIdentifier": {
                    "database": "string",
                    "identifier": "string",
                    "version": "string"
                  },
                  "ontologyTerm": {
                    "term_id": "string",
                    "term": "string"
                  },
                  "experiment": null,
                  "program": {
                    "commandLine": "string",
                    "id": "string",
                    "name": "string",
                    "prevProgramId": "string",
                    "version": "string"
                  },
                  "analysis": {
                    "id": "string",
                    "name": "string",
                    "description": "string",
                    "created": "string",
                    "updated": "string",
                    "type": "string",
                    "software": [],
                    "attributes": null
                  },
                  "nullValue": "NULL_VALUE",
                  "attributes": null,
                  "attributeList": null
                }
              ]
            },
            "property2": {
              "values": [
                {
                  "stringValue": "string",
                  "int64Value": "string",
                  "int32Value": 0,
                  "boolValue": true,
                  "doubleValue": 0,
                  "externalIdentifier": {
                    "database": "string",
                    "identifier": "string",
                    "version": "string"
                  },
                  "ontologyTerm": {
                    "term_id": "string",
                    "term": "string"
                  },
                  "experiment": null,
                  "program": {
                    "commandLine": "string",
                    "id": "string",
                    "name": "string",
                    "prevProgramId": "string",
                    "version": "string"
                  },
                  "analysis": {
                    "id": "string",
                    "name": "string",
                    "description": "string",
                    "created": "string",
                    "updated": "string",
                    "type": "string",
                    "software": [],
                    "attributes": null
                  },
                  "nullValue": "NULL_VALUE",
                  "attributes": null,
                  "attributeList": null
                }
              ]
            }
          }
        }
      },
      "predictedSnsertSize": 0,
      "created": "string",
      "updated": "string",
      "stats": {
        "alignedReadCount": "string",
        "unalignedReadCount": "string",
        "baseCount": "string"
      },
      "programs": [
        {
          "commandLine": "string",
          "id": "string",
          "name": "string",
          "prevProgramId": "string",
          "version": "string"
        }
      ],
      "referenceSetId": "string",
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

A ReadGroupSet is a logical collection of ReadGroups. Typically one ReadGroupSet represents all the reads from one experimental sample.

Properties

Name Type Required Restrictions Description
id string false none The read group set ID.
datasetId string false none The ID of the dataset this read group set belongs to.
name string false none The read group set name.
stats ga4ghReadStats false none ReadStats can be used to provide summary statistics about read data.
readGroups [ga4ghReadGroup] false none The read groups in this set.
attributes ga4ghAttributes false none none

ga4ghReadStats

{
  "alignedReadCount": "string",
  "unalignedReadCount": "string",
  "baseCount": "string"
}

ReadStats can be used to provide summary statistics about read data.

Properties

Name Type Required Restrictions Description
alignedReadCount string(int64) false none The number of aligned reads.
unalignedReadCount string(int64) false none The number of unaligned reads.
baseCount string(int64) false none The total number of bases. This is equivalent to the sum of alignedSequence.length for all reads.

ga4ghSearchReadGroupSetsRequest

{
  "datasetId": "string",
  "name": "string",
  "biosampleId": "string",
  "pageSize": 0,
  "pageToken": "string"
}

This request maps to the body of POST /readgroupsets/search as JSON. TODO: Factor this out to a common API patterns section. - If searching by a resource ID, and that resource is not found, the method will return a 404 HTTP status code (NOT_FOUND). - If searching by other attributes, e.g. name, and no matches are found, the method will return a 200 HTTP status code (OK) with an empty result list.

Properties

Name Type Required Restrictions Description
datasetId string false none The dataset to search.
name string false none Only return read group sets with this name (case-sensitive, exact match).
biosampleId string false none Specifying the id of a Biosample record will return only readgroups with the given biosampleId.
pageSize integer(int32) false none Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
pageToken string false none The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of next_page_token from the previous response.

ga4ghSearchReadGroupSetsResponse

{
  "readGroupSets": [
    {
      "id": "string",
      "datasetId": "string",
      "name": "string",
      "stats": {
        "alignedReadCount": "string",
        "unalignedReadCount": "string",
        "baseCount": "string"
      },
      "readGroups": [
        {
          "id": "string",
          "datasetId": "string",
          "name": "string",
          "description": "string",
          "sampleName": "string",
          "biosampleId": "string",
          "experiment": {
            "id": "string",
            "name": "string",
            "description": "string",
            "messageCreateTime": "string",
            "messageUpdateTime": "string",
            "runTime": "string",
            "molecule": "string",
            "strategy": "string",
            "selection": "string",
            "library": "string",
            "libraryLayout": "string",
            "instrumentModel": "string",
            "instrumentDataFile": "string",
            "sequencingCenter": "string",
            "platformUnit": "string",
            "attributes": {
              "attr": {
                "property1": {
                  "values": [
                    {}
                  ]
                },
                "property2": {
                  "values": [
                    {}
                  ]
                }
              }
            }
          },
          "predictedSnsertSize": 0,
          "created": "string",
          "updated": "string",
          "stats": {
            "alignedReadCount": "string",
            "unalignedReadCount": "string",
            "baseCount": "string"
          },
          "programs": [
            {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            }
          ],
          "referenceSetId": "string",
          "attributes": {
            "attr": {
              "property1": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              },
              "property2": {
                "values": [
                  {
                    "stringValue": "string",
                    "int64Value": "string",
                    "int32Value": 0,
                    "boolValue": true,
                    "doubleValue": 0,
                    "externalIdentifier": {},
                    "ontologyTerm": {},
                    "experiment": {},
                    "program": {},
                    "analysis": {},
                    "nullValue": "NULL_VALUE",
                    "attributes": null,
                    "attributeList": null
                  }
                ]
              }
            }
          }
        }
      ],
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

This is the response from POST /readgroupsets/search expressed as JSON.

Properties

Name Type Required Restrictions Description
readGroupSets [ga4ghReadGroupSet] false none The list of matching read group sets.
nextPageToken string false none The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.

ga4ghSearchReadsRequest

{
  "readGroupIds": [
    "string"
  ],
  "referenceId": "string",
  "start": "string",
  "end": "string",
  "pageSize": 0,
  "pageToken": "string"
}

******************* /reads ********************* This request maps to the body of POST /reads/search as JSON.

If a reference is specified, all queried ReadGroups must be aligned to ReferenceSets containing that same Reference. If no reference is specified, all ReadGroups must be aligned to the same ReferenceSet.*

Properties

Name Type Required Restrictions Description
readGroupIds [string] false none The ReadGroups to search. At least one id must be specified.
referenceId string false none The reference to query. Leaving blank returns results from all references, including unmapped reads - this could be very large.
start string(int64) false none The start position (0-based) of this query. If a reference is specified, this defaults to 0. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
end string(int64) false none The end position (0-based, exclusive) of this query. If a reference is specified, this defaults to the reference's length.
pageSize integer(int32) false none Specifies the maximum number of results to return in a single page. If unspecified, a system default will be used.
pageToken string false none The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of next_page_token from the previous response.

ga4ghSearchReadsResponse

{
  "alignments": [
    {
      "id": "string",
      "readGroupId": "string",
      "fragmentName": "string",
      "improperPlacement": true,
      "duplicateFragment": true,
      "numberReads": 0,
      "fragmentLength": 0,
      "readNumber": 0,
      "failedVendorQualityChecks": true,
      "alignment": {
        "position": {
          "referenceName": "string",
          "position": "string",
          "strand": "STRAND_UNSPECIFIED"
        },
        "mappingQuality": 0,
        "cigar": [
          {
            "operation": "OPERATION_UNSPECIFIED",
            "operationLength": "string",
            "referenceSequence": "string"
          }
        ]
      },
      "secondaryAlignment": true,
      "supplementaryAlignment": true,
      "alignedSequence": "string",
      "alignedQuality": [
        0
      ],
      "nextMatePosition": {
        "referenceName": "string",
        "position": "string",
        "strand": "STRAND_UNSPECIFIED"
      },
      "attributes": {
        "attr": {
          "property1": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          },
          "property2": {
            "values": [
              {
                "stringValue": "string",
                "int64Value": "string",
                "int32Value": 0,
                "boolValue": true,
                "doubleValue": 0,
                "externalIdentifier": {
                  "database": "string",
                  "identifier": "string",
                  "version": "string"
                },
                "ontologyTerm": {
                  "term_id": "string",
                  "term": "string"
                },
                "experiment": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "messageCreateTime": "string",
                  "messageUpdateTime": "string",
                  "runTime": "string",
                  "molecule": "string",
                  "strategy": "string",
                  "selection": "string",
                  "library": "string",
                  "libraryLayout": "string",
                  "instrumentModel": "string",
                  "instrumentDataFile": "string",
                  "sequencingCenter": "string",
                  "platformUnit": "string",
                  "attributes": null
                },
                "program": {
                  "commandLine": "string",
                  "id": "string",
                  "name": "string",
                  "prevProgramId": "string",
                  "version": "string"
                },
                "analysis": {
                  "id": "string",
                  "name": "string",
                  "description": "string",
                  "created": "string",
                  "updated": "string",
                  "type": "string",
                  "software": [
                    "string"
                  ],
                  "attributes": null
                },
                "nullValue": "NULL_VALUE",
                "attributes": null,
                "attributeList": null
              }
            ]
          }
        }
      }
    }
  ],
  "nextPageToken": "string"
}

This is the response from POST /reads/search expressed as JSON.

Properties

Name Type Required Restrictions Description
alignments [ga4ghReadAlignment] false none The list of matching alignment messages, sorted by position. Unmapped reads, which have no position, are returned last.
nextPageToken string false none The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.

ga4ghStrand

"STRAND_UNSPECIFIED"

*Indicates the associated DNA strand for some data item.

Properties

Name Type Required Restrictions Description
anonymous string false none Indicates the associated DNA strand for some data item. - STRAND_UNSPECIFIED: If no strand data is available. - NEG_STRAND: The negative (-) strand. - POS_STRAND: The postive (+) strand.

Enumerated Values

Property Value
anonymous STRAND_UNSPECIFIED
anonymous NEG_STRAND
anonymous POS_STRAND

ga4ghHtsgetResponse

{
  "htsget": {
    "format": "BAM",
    "urls": [
      {
        "url": "string"
      }
    ]
  }
}

Properties

Name Type Required Restrictions Description
htsget ga4ghHtsgetObject false none none

ga4ghHtsgetObject

{
  "format": "BAM",
  "urls": [
    {
      "url": "string"
    }
  ]
}

Properties

Name Type Required Restrictions Description
format string false none Response data format
urls [ga4ghHtsgetUrl] false none An array providing URLs from which raw data can be retrieved.

Enumerated Values

Property Value
format BAM

ga4ghHtsgetUrl

{
  "url": "string"
}

Properties

Name Type Required Restrictions Description
url string false none May be either a https: URL or an inline data: URI. HTTPS URLs require the client to make a follow-up request (possibly to a different endpoint) to retrieve a data block. Data URIs provide a data block inline, without necessitating a separate request.

ga4ghReference

{
  "id": "string",
  "length": "string",
  "md5checksum": "string",
  "name": "string",
  "sourceUri": "string",
  "sourceAccessions": [
    "string"
  ],
  "isDerived": true,
  "sourceDivergence": 0,
  "species": {
    "term_id": "string",
    "term": "string"
  },
  "attributes": {
    "attr": {
      "property1": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      },
      "property2": {
        "values": [
          {
            "stringValue": "string",
            "int64Value": "string",
            "int32Value": 0,
            "boolValue": true,
            "doubleValue": 0,
            "externalIdentifier": {
              "database": "string",
              "identifier": "string",
              "version": "string"
            },
            "ontologyTerm": {
              "term_id": "string",
              "term": "string"
            },
            "experiment": {
              "id": "string",
              "name": "string",
              "description": "string",
              "messageCreateTime": "string",
              "messageUpdateTime": "string",
              "runTime": "string",
              "molecule": "string",
              "strategy": "string",
              "selection": "string",
              "library": "string",
              "libraryLayout": "string",
              "instrumentModel": "string",
              "instrumentDataFile": "string",
              "sequencingCenter": "string",
              "platformUnit": "string",
              "attributes": null
            },
            "program": {
              "commandLine": "string",
              "id": "string",
              "name": "string",
              "prevProgramId": "string",
              "version": "string"
            },
            "analysis": {
              "id": "string",
              "name": "string",
              "description": "string",
              "created": "string",
              "updated": "string",
              "type": "string",
              "software": [
                "string"
              ],
              "attributes": null
            },
            "nullValue": "NULL_VALUE",
            "attributes": null,
            "attributeList": null
          }
        ]
      }
    }
  }
}

*A Reference is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single Reference might represent the human chromosome 1, for instance.

Reference s are designed to be immutable.*

Properties

Name Type Required Restrictions Description
id string false none The reference ID. Unique within the repository.
length string(int64) false none The length of this reference's sequence.
md5checksum string false none The MD5 checksum uniquely representing this Reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).
name string false none The unique name of this reference within the Reference Set (e.g. '22').
sourceUri string false none The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the getReferenceBases() method to obtain sequence bases for a Reference instead of attempting to retrieve this URI.
sourceAccessions [string] false none All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. GCF_000001405.26.
isDerived boolean(boolean) false none A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.
sourceDivergence number(float) false none The sourceDivergence is the fraction of non-indel bases that do not match the reference this message was derived from.
species ga4ghOntologyTerm false none none
attributes ga4ghAttributes false none none

ga4ghReferenceSet

{
  "id": "string",
  "name": "string",
  "md5checksum": "string",
  "species": {
    "term_id": "string",
    "term": "string"
  },
  "description": "string",
  "assemblyId": "string",
  "sourceUri": "string",
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