Parses the ANN field from a VCF file that has been ran through Ensembl's VEP tool or another tool SNPEff. This plugin will format the ANN field to a human readable field in the Primary Data popup info window and will color code Variants based on mutation type.
- Green - Synonymous
- Purple - NonSynonymous
- Red - Truncation/Stop gained
- Blue - Intron/other
For JBrowse 1.11.6+ in the JBrowse/plugins folder, type:
git clone https://github.com/hans-vg/jbplugin-varianteffect.git VariantEffectPlugin
Add this to jbrowse.conf under [GENERAL]
:
[ plugins.VariantEffectPlugin ]
location = plugins/VariantEffectPlugin
Then, in your track configuration, use the following example block:
[ tracks.MyTrack ]
storeClass = JBrowse/Store/SeqFeature/VCFTabix
type = VariantEffectPlugin/View/Track/CanvasEffectVariants
urlTemplate = vcf_files/mysample.vcf.gz
tbiUrlTemplate = vcf_files/mysample.vcf.gz.tbi
maxHeight = 1000
unsafePopup = True
category = Varietal SNPs
key = MyTrackName
Each variant in the loaded VCF file that has the 'ANN' field in the last column will be parsed to display the Variant Effect information in human-readable format in the Info Window box when a variant is clicked in the Browser view. It also changes the default coloring of the Zoomed Out view to be color coded, as well as when you zoom in.