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elsiklab / multivariantviewer

A JBrowse plugin with a custom variant track for multi-VCF files and optionally plotting LD scores
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Create GBrowse style hapmap view #4

Closed cmdcolin closed 8 years ago

cmdcolin commented 8 years ago

This is a screenshot of a gbrowse server running hapmap

gbrowse_haplo_svg_output

It would be useful to have such a thing in this plugin as well

cmdcolin commented 8 years ago

Note that the HapMap gbrowse is now decommissioned http://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/

cmdcolin commented 8 years ago

This has been started (getting the matrix style view)

screenshot-localhost 2016-08-23 16-18-06 screenshot-localhost 2016-08-23 16-18-18

cmdcolin commented 8 years ago

Not sure where to get the LD data

cmdcolin commented 8 years ago

The LD view was obtained dynamically from plink2 from VCF and is available now for testing