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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Datasources for grch38 #149

Closed abought closed 5 years ago

abought commented 6 years ago

Purpose

LZ.js should offer support for grch38 builds. This adds new datasources, as well as global config options to control genome build consistently via a single parameter across all requests.

How to test this

An LZ plot requires 4 core pieces of data. New API services allow us to support each of them.

Compare old and new demo pages for differences. The LD data should largely be a drop in replacement. The following index.html region requires 2 pages of LD data, so verify that all points are colored (pages fill from left to right side of plot): index.html?chrom=10&start=114306616&end=114823842

Genes track may show more or slightly different gene annotations after the version upgrade. Existing deployments often specify a source explicitly, and so they will continue to use the old gencode dataset version.

If the current portal public datasets do not provide build 38 association studies, I can further evaluate via using locuszoom-tabix locally.

TODO