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statgen / locuszoom

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
https://statgen.github.io/locuszoom/
MIT License
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Missing SNP but LD pattern present #263

Closed jcabanad closed 2 years ago

jcabanad commented 2 years ago

Hi,

I'm using your webpage to do some regional plots and I found this situation in one specific region. I have an LD pattern but I don't have the SNP I'm looking for. I don't know if it could be that I don't have this SNP in your reference panel or a bug. Can you please help me. Best,

Judit

Captura de Pantalla 2021-12-10 a les 16 48 49
abought commented 2 years ago

Thanks for the question! The UI is perhaps a bit confusing. I'll try to think of ways to make that easier, and would welcome suggestions based on the description below:

  1. The "Go to region" box finds a position around the specified variant, but it does not ask whether that variant is in a specific study, or tell the plot to do anything else specific to that variant. It just "goes to region".
  2. Once in a region, it draws LD based on either the most significant variant in that region, OR a user-selected variant (each data element has a tooltip with "make ld reference variant" button).