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.
Assoc
LD
Genes
Recomb
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
[x] Standardize mechanisms for querying build across all new and existing data sources
[x] Add support for dynamically selecting which LD population or build to render
[x] Update LD source based on API feedback/ discussion with Daniel
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