README.md

JBrowse plugin for VCF file visualization

JBrowse plugin to visualize VCF file content

Installation

JBrowse dev version installation

# Jbrowse Git: https://github.com/GMOD/jbrowse/releases

# Download JBrowse 1.16.8
wget https://github.com/GMOD/jbrowse/archive/1.16.8-release.tar.gz
# Extract
tar xzf 1.16.8-release.tar.gz
# Rename
mv jbrowse-1.16.8-release jbrowse

My plugin install

cd plugins
git clone https://github.com/arpanda/vcfview.git

load plugin on localhost

http://localhost/jbrowse/jbrowse/?data=plugins/vcfview/test/data
http://localhost/jbrowse/jbrowse/?data=test_vcfview

Demo link

Here is the Demo link: https://arpanda.github.io/vcfview/Jbrowse/?data=plugins/vcfview/test/data

Example config

Here is an example config using our VcfView/Store/SeqFeature/Segmentation class

{
  "tracks": [
    {
      "type": "JBrowse/View/Track/Wiggle/XYPlot",
      "storeClass": "vcfview/Store/SeqFeature/Segmentation",
      "label": "Variants",
      "urlTemplate": "variants.vcf.gz",
      "dpField": "DP",
      "binSize": 1000000,
      "max_score": 10
    }
  ]
}