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Retrieve Variants for Prediction and Chromosome

get

/ohfapi/cg/v3.3/variants/byPrediction/byChromosome

This endpoint supports the retrieval of Variant Identifiers for Chromosome, Start Position, End Position, Assembly/Alignment Identifier, Prediction Type, multiple Prediction Code, Prediction Score and Prediction Comparator. The response fetches Variants Identifiers which are having defined prediction code or score. Both SIFT and PolyPhen (Polymorphism Phenotyping) type data can be searched using this API.

Request

Supported Media Types

• application/json
• application/xml

Query Parameters

• alignmentId: integer(int64)
  Minimum Value: 0

  Assembly/Alignment ID
• chromosome: string
  Chromosome Name. For ex.,'Y'
• endPosition: integer(int64)
  Chromosome End Position
• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from
• predictionCode(optional): array
  Collection Format: multi

  List of Prediction Codes. For ex.,deleterious

  • [0]: string

  {
      "name":"predictionCode",
      "in":"query",
      "description":"List of Prediction Codes. For ex.,deleterious",
      "required":false,
      "type":"array",
      "items":{
          "type":"string"
      },
      "collectionFormat":"multi"
  }

• predictionComparator(optional): string
  Prediction Score Comparator( < , > , = )
• predictionScore(optional): string
  Prediction Score .For ex.,1
• predictionType: string
  Prediction Type. for ex.,SIFT
• startPosition: integer(int64)
  Start location of sequence

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollection

Type: object

Model for paginated collections of data.

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• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• items(optional): array items
  A collection of paged items.
• links(optional): array links
  A collection of links containing hrefs to the current, next, and previous pages as applicable.
• resourceType(optional): string
  Identify the resource type

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"Identify the resource type"
        },
        "items":{
            "type":"array",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/Serializable"
            }
        },
        "count":{
            "type":"integer",
            "format":"int64",
            "description":"Number of objects in the 'items' collection."
        },
        "hasMore":{
            "type":"boolean",
            "description":"A boolean indicating if more pages are available."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object Serializable

{
    "type":"array",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/Serializable"
    }
}

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

Show Source

• Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
    "items":{
        "type":"string"
    }
}

Example:

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Nested Schema : Serializable

Type: object

400 Response

Chromosome End Position is not supplied

404 Response

Variants not found for the Chromosome and Prediction details supplied

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&alignmentId=1&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
   "resourceType":"Variants",
   "items":[
      {
         "identifier":{
            "system":"ODB",
            "value":"536778"
         },
         "variantPrediction":{
            "reference":"/ohfapi/cg/v3.3/variants/536778/variantPredictions"
         }
      },
      {
         "identifier":{
            "system":"ODB",
            "value":"536777"
         },
         "variantPrediction":{
            "reference":"/ohfapi/cg/v3.3/variants/536777/variantPredictions"
         }
      }
   ],
   "count":2,
   "hasMore":false,
   "links":[
      {
         "rel":"self",
         "href":"http://localhost:7010/ohfapi/cg/v3.3/variants/byPrediction/byChromosome?chromosome=CHR&startPosition=10250&endPosition=10251&predictionType=SIFT&predictionScore=1&predictionComparator=<&alignmentId=1&limit=10&offset=0"
      }
   ]
}

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