Extract Flanking Sequence for SNPs

[nathanhaigh]

Users would like to be able to extract sequence information flanking a SNP of interest. This is useful for designing KASP markers.

[nathanhaigh]

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?

[nathanhaigh]

This should be achievable as stated in GMOD/jbrowse#1088. However, I need to check the proposed solution works for me.

[nathanhaigh]

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.