OpenAPI / Swagger documentation
Interactive and always up to date API documentation can be found here: https://api.genebe.net/cloud/gb-api-doc/swagger-ui/index.html .
Below is more human edited API documentation, that may be outdated, but may contain more human comments than OpenAPI.
Additional comments to the endpoints can be found on the other pages of this documentation.
Ask for multiple variants at once
Plese do not ask for more than 1000 entries in one query. Body example: '[{"chr":"22", "pos":28695868, "ref":"AG", "alt":"A"}]'
| Method | URL |
|---|
| POST | /api-public/v1/variants |
Parameters
| Name | In | Description | Required |
|---|
| genome | query | | Required |
| useRefseq | query | Use transcripts from Refseq. | Optional |
| useEnsembl | query | Use transcripts from Ensembl. | Optional |
| omitAcmg | query | Don't add ACMG scores in the output | Optional |
| omitCsq | query | Don't add consequences in the output. | Optional |
| omitBasic | query | Don't add basic annotations (GnomAD frequencies etc) in the output. | Optional |
| omitAdvanced | query | Don't add advanced annotations (ClinVar frequencies etc) in the output. | Optional |
| omitNormalization | query | Don't normalize variants. Use only if you are sure they are normalized already. | Optional |
| allGenes | query | Annotate for all genes in this region. | Optional |
| customAnnotations | query | Comma delimited list of custom annotations to be applied. Consult with documentation for recognized values. | Optional |
annotator | query | Which annotator to use. Please leave empty for now. | Optional |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| variants | array | |
| message | string | |
Translate SPDI to genome coordinates, single variant
For parsing multiple variants please use POST. It is many times faster. Currently supports only hg38.
| Method | URL |
|---|
| GET | /api-public/v1/spdi |
Parameters
| Name | In | Description | Required |
|---|
| spdi | query | | Required |
| genome | query | | Optional |
Response (404)
Response (403)
Response (200)
Translate SPDI to genome coordinates, multiple variants. Currently supports only hg38.
| Method | URL |
|---|
| POST | /api-public/v1/spdi |
Parameters
| Name | In | Description | Required |
|---|
| genome | query | | Optional |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
LiftOver single variant
For lifting multiple variants please use POST. It is many times faster.
| Method | URL |
|---|
| GET | /api-public/v1/liftover |
Parameters
| Name | In | Description | Required |
|---|
| query | query | | Required |
| from | query | Source human genome version, one of hg19, hg38, t2t. | Required |
| dest | query | Destination human genome version, one of hg19, hg38, t2t. | Required |
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| from | string | |
| dest | string | |
| variants | array | |
| error | string | |
LiftOver multiple variants
LiftOver simple variants between hg19/hg38/2t2. This is a very simple service. Returns at most one position for one query.
| Method | URL |
|---|
| POST | /api-public/v1/liftover |
Parameters
| Name | In | Description | Required |
|---|
| from | query | Source human genome version, one of hg19, hg38, t2t. | Required |
| dest | query | Destination human genome version, one of hg19, hg38, t2t. | Required |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| from | string | |
| dest | string | |
| variants | array | |
| error | string | |
Translate HGVS to genome coordinates, single variant
For parsing multiple variants please use POST. It is many times faster. We recognize only c, n, g and m HGVS strings. Parse may not work for p. Some special cases of HGVS as well as less popular transcripts may not be recognized.
| Method | URL |
|---|
| GET | /api-public/v1/hgvs |
Parameters
| Name | In | Description | Required |
|---|
| hgvs | query | | Required |
| genome | query | | Optional |
Response (404)
Response (403)
Response (200)
Translate HGVS to genome coordinates, multiple variants
We recognize only c, n, g and m HGVS strings. Parse may not work for p. Some special cases of HGVS as well as less popular transcripts may not be recognized.
| Method | URL |
|---|
| POST | /api-public/v1/hgvs |
Parameters
| Name | In | Description | Required |
|---|
| genome | query | | Optional |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Method | URL |
|---|
| POST | /api-public/v1/files |
Parameters
| Name | In | Description | Required |
|---|
| analysisId | query | TODO | Required |
| fileType | query | | Optional |
| sequencingId | query | | Optional |
| projectName | query | | Optional |
| analysisName | query | | Optional |
| deduplicate | query | | Optional |
| genome | query | | Optional |
Request Body
| Field | Type | Description | Required |
|---|
| file | string | | Required |
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| id | string | |
| name | string | |
| fileType | string | |
| analysisId | array | |
Translate SPDI, HGVS, rs or other to genome coordinates, multiple variants. Currently supports only hg38.
For parsing multiple variants please use POST. It is many times faster. Currently supports only hg38.
| Method | URL |
|---|
| GET | /api-public/v1/convert |
Parameters
| Name | In | Description | Required |
|---|
| id | query | | Required |
| genome | query | | Optional |
Response (404)
Response (403)
Response (200)
Translate SPDI, HGVS, rs or other to genome coordinates, multiple variants. Currently supports only hg38.
| Method | URL |
|---|
| POST | /api-public/v1/convert |
Parameters
| Name | In | Description | Required |
|---|
| genome | query | | Optional |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
Describe single CNV variant
For annotating multiple CNV variants please use POST. It is many times faster.
| Method | URL |
|---|
| GET | /api-public/v1/cnvs |
Parameters
| Name | In | Description | Required |
|---|
| chr | query | | Required |
| start | query | | Required |
| end | query | | Required |
| svType | query | | Required |
| omitAcmg | query | Don't add ACMG scores in the output | Optional |
| genome | query | | Required |
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| cnvs | array | |
| message | string | |
Ask for multiple CNV variants at once
Do not ask for more than 1000 entries in one query. Body example: '[{"chr":"7", "start":72846244, "end":74187855}]'
| Method | URL |
|---|
| POST | /api-public/v1/cnvs |
Parameters
| Name | In | Description | Required |
|---|
| omitAcmg | query | Don't add ACMG scores in the output | Optional |
| genome | query | | Required |
Request Body
| Field | Type | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| cnvs | array | |
| message | string | |
Short information and statistics about the asker: Who am I? Includes information about the number of requests done.
| Method | URL |
|---|
| GET | /api-public/v1/whoami |
Parameters
| Name | In | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| identifier | string | |
| ip | string | |
| accountId | integer | |
| accountPlan | string | |
| reqGetVarApi | integer | |
| reqPostVarApi | integer | |
| varPostVarApi | integer | |
| organizations | array | |
Describe single variant
For annotating multiple variants please use POST. It is many times faster.
| Method | URL |
|---|
| GET | /api-public/v1/variant |
Parameters
| Name | In | Description | Required |
|---|
| chr | query | | Required |
| pos | query | | Required |
| ref | query | | Required |
| alt | query | | Required |
| transcript | query | Force usage of this transcript in ACMG score assignment. | Optional |
| gene_symbol | query | Force usage of this gene in ACMG score assignment. | Optional |
| annotator | query | Which annotator to use. Please leave empty for now. | Optional |
| useRefseq | query | Use transcripts from Refseq. | Optional |
| useEnsembl | query | Use transcripts from Ensembl. | Optional |
| omitAcmg | query | Don't add ACMG scores in the output | Optional |
| omitCsq | query | Don't add consequences in the output. | Optional |
| omitBasic | query | Don't add basic annotations (GnomAD frequencies etc) in the output. | Optional |
| omitAdvanced | query | Don't add advanced annotations (ClinVar frequencies etc) in the output. | Optional |
| omitNormalization | query | Don't normalize variants. Use only if you are sure they are normalized already. | Optional |
| allGenes | query | Annotate for all genes in this region. | Optional |
| customAnnotations | query | Comma delimited list of custom annotations to be applied. Consult with documentation for recognized values. | Optional |
| genome | query | | Required |
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| variants | array | |
| message | string | |
| Method | URL |
|---|
| GET | /api-public/v1/genes |
Parameters
| Name | In | Description | Required |
|---|
| hgncId | query | | Optional |
| symbol | query | | Optional |
Response (404)
Response (403)
Response (200)
| Field | Type | Description |
|---|
| id | string | |
| symbol | string | |
| ensemblId | string | |
| hgncId | integer | |
| name | string | |
| refseqId | string | |
| ncbiId | integer | |
| omimId | string | |
| uniprotId | string | |
| vegaId | string | |
| geneGroup | string | |
| previousSymbols | array | |
| chr | string | |
| start | integer | |
| end | integer | |
| inheritance | string | |
| clinvarGeneSummary | object | |
| maneSelectEnsemblId | string | |
| maneSelectRefSeqId | string | |
| geneCcData | array | |
| geneDbnsfpData | object | |
| geneGnomadData | object | |
| geneCgdData | object | |
| Method | URL |
|---|
| GET | /api-public/v1/files/sample/{id}/input/{fileid}/{name} |
Parameters
| Name | In | Description | Required |
|---|
| id | path | | Required |
| fileid | path | | Required |
| name | path | | Required |
Response (404)
Response (403)
Response (200)
| Method | URL |
|---|
| GET | /api-public/v1/files/sample/{id}/file/{name} |
Parameters
| Name | In | Description | Required |
|---|
| id | path | | Required |
| name | path | | Required |
Response (404)
Response (403)
Response (200)
| Method | URL |
|---|
| GET | /api-public/v1/files/sample/{id}/doc/{name} |
Parameters
| Name | In | Description | Required |
|---|
| id | path | | Required |
| name | path | | Required |
Response (404)
Response (403)
Response (200)
| Method | URL |
|---|
| GET | /api-public/file-ping |
Parameters
| Name | In | Description | Required |
|---|
Response (404)
Response (403)
Response (200)
| Method | URL |
|---|
| DELETE | /api-public/v1/files/{fileId} |
Parameters
| Name | In | Description | Required |
|---|
| fileId | path | | Required |
Response (404)
Response (403)
Response (200)