Open nathanhaigh opened 6 years ago
This would require implementing a right-click context menu for features derived from a VCF track. The simplest case, would be to simply extract the CS reference sequences +/- 50bp around the SNP.
Would variants that fall within this window also need to be incorporated into the extracted sequence?
This should be achievable as stated in https://github.com/GMOD/jbrowse/issues/1088. However, I need to check the proposed solution works for me.
So the issue is the CanvasVariants
track can't be set to displayMode = collapsed
. The following type of code can thus be used:
displayMode = normal
showLabels = false
menuTemplate+=json:{}
menuTemplate+=json:{}
menuTemplate+=json:{}
menuTemplate+=json:{"label": "Retrieve flanking sequence", "iconClass" : "dijitIconBookmark", "action" : "contentDialog", "content" : "function(track,feature){return track.browser.plugins.FeatureSequence.callFxn(track, feature); }"}
Now just need to write a plugin, cribbing from FeatureSequence
plugin.
Users would like to be able to extract sequence information flanking a SNP of interest. This is useful for designing KASP markers.