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
csiUrlTemplate = vcf_files/mysample.vcf.gz.csi
maxHeight = 1000
unsafePopup = True
category = Varietal SNPs
key = MyTrackName
metadata.Description = 1000 Wheat Exomes - SNPeff
metadata.SNP-Colors = <span style='background-color:red'> </span> <span style='color:red'>(Red)</span> - SNPs with truncations<br><span style='background-color:purple'> </span> <span style='color:purple'>(Violet)</span> - amino acid changes<br><span style='background-color:green'> </span> <span style='color:green'>(Green)</span> - silent mutations<br><span style='background-color:blue'> </span> <span style='color:blue'>(Blue)</span> - outside gene regions
Note use of CSI index, instead of TBI for larger genomes. Generated by tabix --csi option.
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.