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Retrieve Variants for Variant Effect and Chromosome

get

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

This endpoint supports the retrieval of Variant Identifiers for Variant Effect, Chromosome, Start Position, End Position and Assembly/Alignment Identifier.

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
• startPosition: integer(int64)
  Start location of sequence
• variantEffect: string
  Variant Effect

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.

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• 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

Filter Variants input is not valid

404 Response

Variants not found for the Chromosome and VariantEffect supplied

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "items":[
  {
  "identifier":"138260072"
  }
  ]
  "count": 1,
  "hasMore": false,
  "links" : [ {
     "rel" : "self",
     "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byEffect/byChromosome?alignmentId=1&chromosome=CHR&startPosition=10250&endPosition=10251&variantEffect=synonymous&limit=10&offset=0"
   } ] 
}

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