HiGlass VCF Track

Track for viewing VCF files.

Note: This is the source code for the pileup only! You might want to check out the following repositories as well:

• HiGlass viewer: https://github.com/higlass/higlass
• HiGlass server: https://github.com/higlass/higlass-server
• HiGlass docker: https://github.com/higlass/higlass-docker

Installation

npm install higlass-vcf

Usage

The live scripts can be found at:

• https://unpkg.com/[email protected]/dist/higlass-vcf.min.js

Client

1. Make sure you load this track prior to hglib.js. For example:

<script src="https://unpkg.com/[email protected]/dist/higlass-vcf.min.js"></script>
<script src="hglib.js"></script>
<script>
  ...
</script>

2. Now, configure the track in your view config and be happy!

{
  "editable": true,
  "trackSourceServers": [
    "http://higlass.io/api/v1"
  ],
  "exportViewUrl": "/api/v1/viewconfs",
  "views": [
    {
      "initialXDomain": [
        0,
        100000
      ],
      "tracks": {
        "top": [
          {
            "type": "vcf",
            "height": 180,
            "uid": "FylkvVBTSumoJ959HT4-5A",
            "data": {
              "type": "vcf",
              "url": "https://pkerp.s3.amazonaws.com/public/HG002_SVs_Tier1_v0.6.vcf.gz",
              "chromSizesUrl": "https://resgen.io/api/v1/chrom-sizes/?id=cNE4StljSAK9lK3amECl-A"
            },
          }
        ]
      }
    }
  ]
}

Support

For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack

Development

Installation

$ git clone https://github.com/higlass/higlass-vcf-track && higlass-vcf-track
$ npm install

Commands

Developmental server: npm start Production build: npm run build