List markers available on a file

❗️

Heads Up!

This page documents the Advance Access version (think "beta" but with fewer bugs) of the Marker functionality.

Request

This call lists the genetic markers available on a single BAM file. Note that these markers can also be examined via the Seven Bridges Genome Browser.

https://api.sbgenomics.com//v2/genome/markers?file={file_id}
https://eu-api.sbgenomics.com/genome/markers?file={file_id}

Example request

GET /v2/genome/markers?file=592444771c94679800e99c23 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f75
X-SBG-Advance-Access: advance
from sevenbridges import Api

api = Api(url='https://api.sbgenomics.com/v2',
          token='3259c50e1ac5426ea8f1273259740f74',
          advance_access=True)

# send GET request to SB API
markers = api.markers.query(file='592444771c94679800e99c23')

for marker in markers:
    print(marker.id, marker.name)

Header Fields

Name

Description

X-SBG-Auth-Token
required

Your Seven Bridges Platform authentication token.

Content-Type
required

application/json

X-SBG-Advance-Access
required

advance

Query parameters

Name

Description

file

This is the file ID for the BAM file whose markers you wish to return. Files are specified by their IDs, which you can obtain by making the API call to list files in a project.

Response

See a list of Seven Bridges Platform-specific response codes that may be contained in the body of the response.

Example response body

The response body contains information about the specified marker.

{
  "href": "http://api.sbgenomics.com/v2/genome/markers?file=592444771c94679800e99c23”,
  "items": [
    {
      "href": "http://api.sbgenomics.com/v2/genome/markers/59244b2a92bd172e013a1a8c",
      "id": "59244b2a92bd172e013a1a8c",
      "name": "Example Marker"
    },
    {
      "href": "http://api.sbgenomics.com/v2/genome/markers/59254a6892bd172e013a1a90",
      "id": "59254a6892bd172e013a1a90",
      "name": "Example Marker 1"
    }
}

Interpreting the response body

Consult the table below to interpret the items object in the response above.

Key

Description of value

href

This is a link to a specific genetic marker available on the BAM file queried. Use this to Get details for a single marker.

id

This is the marker_id for a specific genetic marker available on the BAM file queried. Use this to Get details for a single marker.

name

This is the name of a genetic marker available on the BAM file queried.