As study locus can be generated by a number of processes yielding quite different flavors of the same fundamental data type, plus the credible sets can be calculated via different methods (locus from the same Finngen study can contain credible sets based on SuSiE and PICS). When these study-locus datasets are merged together, this information needs to be propagated somehow also this is not study level information but specific for the given study-locus.
The idea was to add the following struct to the study locus schema. Example:
The method would tell how the locus was identified: curation (pre-ld expanded GWAS curated data), distance based clumping (from summary stats), LD based clumping (after the previous two), PICS finemapping, SuSiE finemapping
Source would tell where the data is coming from: FINNGEN finemapping or GWAS Catalog
It's not exactly clear what and how to store in these fields, however something needs to be propagated to make sure at the end each study locus is fully tractable.
Also besides adding this value to the schema, we need to make sure: each method that outputs study locus updates these fields.
As study locus can be generated by a number of processes yielding quite different flavors of the same fundamental data type, plus the credible sets can be calculated via different methods (locus from the same Finngen study can contain credible sets based on SuSiE and PICS). When these study-locus datasets are merged together, this information needs to be propagated somehow also this is not study level information but specific for the given study-locus.
The idea was to add the following struct to the study locus schema. Example:
curation
(pre-ld expanded GWAS curated data),distance based clumping
(from summary stats),LD based clumping
(after the previous two),PICS finemapping
,SuSiE finemapping
FINNGEN finemapping
orGWAS Catalog
It's not exactly clear what and how to store in these fields, however something needs to be propagated to make sure at the end each study locus is fully tractable.
Also besides adding this value to the schema, we need to make sure: each method that outputs study locus updates these fields.