Dataset Specification

Contents

1. Overview
2. JSON Structure

Please note that this document is a work in progress, with large sections of content missing.

Overview

The ambition for Pretzel is the flexibility to handle the range of structured genetic datasets commonly used today. Work on this capability is in active development. Currently, a specialised dataset specification has been used for development of Pretzel, as summarised in this document.

JSON Structure

Two example genetic maps that can be consumed by Pretzel are outlined below. Note that this specification is likely to change soon for more flexibility :

# cat resources/example_map1.json
{ "geneticmap":
  {
    "name": "MyMap1",
    "chromosomes":
    [
      {
      "name": "MrChr",
      "markers":
        [
          {
          "name": "markerA",
          "position": 1
          },
          {
          "name": "markerB",
          "position": 1.5
          }
        ]
      }
    ]
  }
}

# cat resources/example_map2.json
{ "geneticmap":
  {
    "name": "MyMap2",
    "chromosomes":
    [
      {
      "name": "MyChr",
      "markers":
        [
          {
          "name": "markerA",
          "position": 0
          },
          {
          "name": "markerB",
          "position": 1.3
          }
        ]
      }
    ]
  }
}