LiftOver, HGVS, dbSNP and other variant converter

Information about converter and liftover

Usage in python is described in pandas chapter.

Until there is no better documentation, visit the OpenAPI documentation here:

For liftover:

https://api.genebe.net/cloud/gb-api-doc/swagger-ui/index.html#/liftover-public-controller/lift_1

For HGVS and other converter:

https://api.genebe.net/cloud/gb-api-doc/swagger-ui/index.html#/variant-converter-public-controller/parseSingle

Example GET

Example of converting dbSNP rs11 to VCF-like position:

# convert dbSNP id:
curl -X 'GET' \
  'https://api.genebe.net/cloud/api-public/v1/convert?id=rs11&genome=hg38' \
  -H 'accept: */*'

[
  {
    "variants": [
      {
        "genome": "hg38",
        "chr": "7",
        "pos": 11324574,
        "ref": "C",
        "alt": "T"
      }
    ]
  }
]

Examples

Example of converting HGVS NM_018136.4:c.567_569del to VCF-like position:

# convert dbSNP id:
curl -X 'GET' \
  'https://api.genebe.net/cloud/api-public/v1/convert?id=NM_018136.4:c.567_569del&genome=hg38' \
  -H 'accept: */*'

[
  {
    "variants": [
      {
        "genome": "hg38",
        "chr": "1",
        "pos": 197143682,
        "ref": "GCTC",
        "alt": "G"
      }
    ]
  }
]

Example of converting deletion 22-28695869-G- to VCF-like position:

# convert dbSNP id:
curl -X 'GET' \
  'https://api.genebe.net/cloud/api-public/v1/convert?id=22-28695869-G-&genome=hg38' \
  -H 'accept: */*'

[
  {
    "variants": [
      {
        "genome": "hg38",
        "chr": "22",
        "pos": 28695868,
        "ref": "AG",
        "alt": "A"
      }
    ]
  }
]

Endpoint should also work well for p. HGVS or even query like AGT M259T. Be careful though, this conversion may not always work as exptected.

curl -X 'GET' \
  'https://api.genebe.net/cloud/api-public/v1/convert?id=AGT%20M259T&genome=hg38' \
  -H 'accept: */*'

[
  {
    "variants": [
      {
        "genome": "hg38",
        "chr": "1",
        "pos": 230710048,
        "ref": "A",
        "alt": "G"
      }
    ]
  }
]