Variant track configuration

• defaultRendering - options: 'pileup' or 'svg'. default 'svg'
• adapter - a variant type adapter config e.g. a VcfTabixAdapter

Example config:

{
  "type": "VariantTrack",
  "trackId": "my track",
  "name": "My Variants",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "vcfGzLocation": {
      "uri": "http://yourhost/file.vcf.gz",
      "locationType": "UriLocation"
    },
    "index": {
      "location": {
        "uri": "http://yourhost/file.vcf.gz.tbi",
        "locationType": "UriLocation"
      }
    }
  }
}

VcfTabixAdapter configuration options

• vcfGzLocation - a 'file location' for the BigWig
• index - a subconfiguration schema containing
  • indexType: options TBI or CSI. default TBI
  • location: the location of the index

Example VcfTabixAdapter adapter config:

{
  "type": "VcfTabixAdapter",
  "vcfGzLocation": {
    "uri": "http://yourhost/file.vcf.gz",
    "locationType": "UriLocation"
  },
  "index": {
    "location": {
      "uri": "http://yourhost/file.vcf.gz.tbi",
      "locationType": "UriLocation"
    }
  }
}