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ldserver API

API specification

Correlation types

These are the various correlation measures supported by the server. Examples are r2 and D'.

Request

GET /correlations

Response

{
  "data": [
    {
      "description": "",
      "label": "r",
      "name": "r",
      "type": "LD"
    },
    {
      "description": "",
      "label": "r^2",
      "name": "rsquare",
      "type": "LD"
    },
    {
      "description": "",
      "label": "covariance",
      "name": "cov",
      "type": "Covariance"
    }
  ],
  "error": null
}

Genome builds

Get a list available genome builds.

Request

GET /genome_builds

Response

{
  "data": [
    "GRCh37",
    "GRCh38"
  ],
  "error": null
}

References

Get a list of all available reference panels.

Request

GET /genome_builds/<build>/references

Response

{
  "data": [
    {
      "description": "1000 Genomes Project Phase 3",
      "name": "1000G"
    }
  ],
  "error": null
}

Populations

Request

GET /genome_builds/<build>/references/<reference>/populations

Response

{
  "data": [
    "AFR",
    "ALL",
    "AMR",
    "EAS",
    "EUR",
    "SAS"
  ],
  "error": null
}

Pair-wise region correlations

Request

GET /genome_builds/GRCh37/references/1000G/populations/AFR/regions

Parameters

Param Type Examples Details
chrom string "10", "X"
start int 1
stop int 9
correlation string "rsquare" Corresponds to /correlations types
limit int 1000 Limit the number of records
format string "classic" or "compact" Classic is default. Compact is much smaller, but slightly harder to parse
precision int 4 Limits precision of LD values

Response

If using default format (classic):

{
  "data": {
    "variant1": [
      "10:114550501_G/A",
      "10:114550501_G/A",
      "10:114550501_G/A",
      "10:114550523_G/GT",
      "10:114550523_G/GT",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C"
    ],
    "chromosome1": [
      "10",
      "10",
      "10",
      "10",
      "10",
      "10"
    ],
    "position1": [
      114550501,
      114550501,
      114550501,
      114550523,
      114550523,
      114550588
    ],
    "variant2": [
      "10:114550523_G/GT",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C",
      "10:114550600_A/G",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C",
      "10:114550600_A/G",
      "10:114550600_A/G"
    ],
    "chromosome2": [
      "10",
      "10",
      "10",
      "10",
      "10",
      "10"
    ],
    "position2": [
      114550523,
      114550588,
      114550600,
      114550588,
      114550600,
      114550600
    ],
    "correlation": [
      0.002376697026193142,
      0.00014225491031538695,
      0.0006637412589043379,
      0.03565419092774391,
      0.04548444598913193,
      0.0029309114906936884
    ]
  },
  "error": null,
  "next": null
}

If using format=compact:

{
  "data": {
    "variants": [
      "10:114550501_G/A",
      "10:114550523_G/GT",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C",
      "10:114550600_A/G"
    ],
    "chromosomes": [
      "10",
      "10",
      "10",
      "10"
    ],
    "positions": [
      114550501,
      114550523,
      114550588,
      114550600
    ],
    "offsets": [
      1,
      2,
      3,
      -2147483648
    ],
    "correlations": [
      [
        0.002376697026193142,
        0.00014225491031538695,
        0.0006637412589043379
      ],
      [
        0.03565419092774391,
        0.04548444598913193
      ],
      [
        0.0029309114906936884
      ],
      []
    ]
  },
  "error": "",
  "next": ""
}

Reference variant correlations

Retrieves correlations between a reference variant and all others in a defined region.

Request

GET /genome_builds/GRCh37/references/1000G/populations/AFR/regions

Parameters

Param Type Examples Details
chrom string "10", "X"
start int 1
stop int 9
variant string "10:1414141_A/T" Reference variant
correlation string "rsquare" Corresponds to /correlations types
limit int 1000 Limit the number of records
format string "classic" or "compact" Classic is legacy format, newer clients should prefer "compact"
precision int 4 Limits precision of LD values

Response

If using default/classic format:

{
  "data": {
    "variant1": [
      "10:114758349_C/T",
      "10:114758349_C/T",
      "10:114758349_C/T",
      "10:114758349_C/T",
      "10:114758349_C/T",
      "10:114758349_C/T"
    ],
    "chromosome1": [
      "10",
      "10",
      "10",
      "10",
      "10",
      "10"
    ],
    "position1": [
      114758349,
      114758349,
      114758349,
      114758349,
      114758349,
      114758349
    ],
    "variant2": [
      "10:114550498_G/A",
      "10:114550501_G/A",
      "10:114550523_G/GT",
      "10:114550586_C/T",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C",
      "10:114550600_A/G"
    ],
    "chromosome2": [
      "10",
      "10",
      "10",
      "10",
      "10",
      "10"
    ],
    "position2": [
      114550498,
      114550501,
      114550523,
      114550586,
      114550588,
      114550600
    ],
    "correlation": [
      5.892965054954402e-05,
      2.6653198801795952e-05,
      0.0002563385060057044,
      0.0001682174624875188,
      0.0007479109917767346,
      0.0004545401025097817
    ]
  },
  "error": null,
  "next": null
}

If using format=compact:

{
  "data": {
    "index_variant": "10:114758349_C/T",
    "index_chromosome": "10",
    "index_position": 114758349,
    "variants": [
      "10:114550498_G/A",
      "10:114550501_G/A",
      "10:114550523_G/GT",
      "10:114550586_C/T",
      "10:114550588_CTCATAGCTGGAAGTCCCCTGGTAGGAGGA/C",
      "10:114550600_A/G"
    ],
    "chromosomes": [
      "10",
      "10",
      "10",
      "10",
      "10",
      "10"
    ],
    "positions": [
      114550498,
      114550501,
      114550523,
      114550586,
      114550588,
      114550600
    ],
    "correlations": [
      5.892965054954402e-05,
      2.6653198801795952e-05,
      0.0002563385060057044,
      0.0001682174624875188,
      0.0007479109917767346,
      0.0004545401025097817
    ]
  },
  "error": "",
  "next": ""
}