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CNVpytorVCF

CNVpytor plugin for JBrowse

Demo example for CNVpytor export and CNVpytorVCF plugin

Demo page with Hg19 reference: https://abyzovlab.github.io/CNVpytorVCF/JBrowse/

CNVpytor export

Read depth and BAF analysis is done for HepG2 genome using CNVpytor and both BAM and VCF file are used here. Three different bin sizes (i.e.; 10K, 100K, 1000K) are used for detailed understanding. JBrowse page automatically selects the bin size based on the length of the selected region. Here, only 100K bin size is kept.

CNVpytorVCF plugin

Demo example takes the HepG2 vcf file, which supplied together with this plugin. Currently, it takes 100k as bin size. Plugin does on the fly calculation for read depth and BAF analysis. A new vcf file can be loaded using the tools menu.

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

Plugin install: To install a JBrowse plugin, copy the plugin in the JBrowse plugin directory

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

Dependencies

To Install ml-levenberg-marquardt, use by the following command in the JBrowse root directory

yarn add ml-levenberg-marquardt

load plugin on localhost

http://localhost/jbrowse/?data=plugins/CNVpytorCNV/test/data