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hans-vg / jbplugin-varianteffect

A JBrowse plugin to display the Variant Effect information in the "ANN" field of a VCF file
MIT License
6 stars 4 forks source link

Updated config to support JBrowse 1.16.6 #3

Closed enuggetry closed 5 years ago

enuggetry commented 5 years ago

in jbrowse.conf, add: 

[ plugins.VariantEffectPlugin ]
location = plugins/VariantEffectPlugin/js

Added legend. Note use of CSI index, instead of TBI. Generated by tabix --csi option. This alleviates an index warning in JBrowse 1.16.6. I guess the integer indexes overflow.

[ tracks.vcf-eff ]
metadata.category = 1000 Wheat Exomes
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
type = VariantEffectPlugin/View/Track/CanvasEffectVariants
urlTemplate    = vcf_files/1000-170208_AllChr-IWGSC_WGA_v1_SNPList.ann.HC.vcf.gz
csiUrlTemplate = vcf_files/1000-170208_AllChr-IWGSC_WGA_v1_SNPList.ann.HC.vcf.gz.csi
key = SNP effects
metadata.Description = 1000 Wheat Exomes - SNPeff
unsafePopup = True
metadata.SNP-Colors = <span style='background-color:red'>&nbsp;</span> <span style='color:red'>(Red)</span> - SNPs with truncations<br><span style='background-color:purple'>&nbsp;</span> <span style='color:purple'>(Violet)</span> - amino acid changes<br><span style='background-color:green'>&nbsp;</span> <span style='color:green'>(Green)</span> - silent mutations<br><span style='background-color:blue'>&nbsp;</span> <span style='color:blue'>(Blue)</span> - outside gene regions
hans-vg commented 5 years ago

Thank you. I've updated the readme.