A JBrowse plugin that adds some custom glyphs for variants and GWAS data
It could be useful to only show labels above a certain score for style->label, e.g.
"style": { "label": "function(feature) { return -Math.log(feature.get('score'))>50 ? feature.get('name') : null; }" }
The circle glyph is used just for convenience, but it is by nature larger than the actual variant in genome coordinates on the screen, which can cause minor rendering issues like having half circles at block boundaries
The useMyVariantInfo and useEnsemblR2 are exclusive to one another, as they both use click action
Using the "BEDTabix" class
{
"maxFeatureScreenDensity": 6,
"storeClass" : "JBrowse/Store/SeqFeature/BEDTabix",
"urlTemplate" : "HDL_pval_name.sort.bed.gz",
"label" : "HDL_pvals",
"type" : "GWASViewer/View/Track/VariantPlotter"
}
Using a track loaded with flatfile-to-json.pl (GWASViewer can load GFF file with scores, or a BED with a score column)
{
"maxFeatureScreenDensity": 6,
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"urlTemplate" : "tracks/HDL_pval_name/{refseq}/trackData.json",
"label" : "HDL_pvals",
"type" : "GWASViewer/View/Track/VariantPlotter"
}
Note you can use flatfile-to-json.pl with --trackType "GWASViewer/View/Track/VariantPlotter" to automatically set this up
Basic GWASViewer track
Shows track with useEnsemblR2
enabled, which fetches R^2 from Ensembl for variants in linkage with a variant that is clicked (pink diamond)
Still in beta! Feel free to provide feedback
Test GWASViewer tracks are in the test/data/ directory, visit http://localhost/jbrowse/?data=plugins/GWASViewer/test/data or similar to view