GMOD/myvariantviewer

Name: myvariantviewer

Owner: Generic Model Organism Database Project

Description: A JBrowse plugin for viewing info from myvariant.info

Forked from: elsiklab/myvariantviewer

Created: 2016-03-08 00:11:24.0

Updated: 2016-03-10 23:56:07.0

Pushed: 2016-03-10 22:01:54.0

Homepage: null

Size: 528

Language: JavaScript

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README

myvariantviewer

A JBrowse plugin that fetches info from MyVariant.info and MyGene.info and displays them.

Example configuration

Fetch genes and variants from hg19:

  {
     "storeClass" : "MyVariantViewer/Store/SeqFeature/Genes",
     "urlTemplate" : "http://mygene.info/v2/query?q=hg19.{refseq}:{start}-{end}&fields=all&email=colin.diesh@gmail.com&size=1000",
     "subParts" : [
        "exon"
     ],
     "type" : "CanvasFeatures",
     "label" : "MyGene.info",
     "hg19" : true
  },
  {
     "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants",
     "urlTemplate" : "query?q={refseq}:{start}-{end}&size=1000&fetch_all=true&email=colin.diesh@gmail.com",
     "baseUrl": "http://myvariant.info/v1/",
     "type" : "CanvasFeatures",
     "label" : "MyVariant.info"
  }

Note: we now use a “scroll query” for variants, so fetch_all should be supplied in the URL template, and the baseUrl should be separate from urlTemplate in the Variants track

Only query from a specific data source

Example to only query variants from clinvar (combining the exists-in clinvar query with fields=clinvar return values)

  {
     "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants",
     "baseUrl" : "http://myvariant.info/v1/",
     "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:clinvar&size=1000&fetch_all=true&email=colin.diesh@gmail.com&fields=clinvar",
     "type" : "CanvasFeatures",
     "label" : "MyVariant.info clinvar"
  }

See https://github.com/cmdcolin/myvariantviewer/blob/master/test/trackList.json for more

Screenshots