Making LD annotation source agnostic

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Making LD annotation source agnostic #3094

Closed DSuveges closed 9 months ago

DSuveges commented 9 months ago

Currently the logic to resolve ld in the study locus dataset is tied to gwas catalog, however this should be general method applicable to any study locus given the population structure from the study index is resolvable.

There are few things we need to consider:

A study might not have any population info.
Although all LD sets we currently have coming from GnomAD, this might not be always the case, this logic shouuld also generalized.

DSuveges commented 9 months ago

Along these lines:

Generalizing ld population map

Also, the resulting mapping, for the sake of data provenance, should be stored in the study table.

DSuveges commented 9 months ago

Points of updates:

[x] Adding new function to the sared study index logic
[x] Adding tests to the new functions.
[x] Updating/removing tests pointing to old logic.
[x] LD population to GWAS Catalog Studies.
[x] LD population to FINNGEN studies.
[x] LD population to UKBB studies.