GWAS Catalog contains only chrom and pos, as well as rsid and sometimes effect allele, never effect + ref.
Previous solution
Fetch alleles from dbSNP REST API.
Pain points with that approach
Server is quite slow
Server does not seem to hold up under a lot of load, getting lots of http 500 responses
Dependency on external resource, so moving autoreporting to a closed environment is a no-go currently.
Solution
Change dbSNP to one of our annotations, e.g. the gnomad annotation, that has alleles for a wide range of variants. We could also take allele frequencies for fin, nfsee populations to e.g. filter the hits based on whether those variants are available in the Finnish population, etc.
Steps
Change GWCatalog DAOs to use a separate annotation file instead of dbSNP
Problem
GWAS Catalog contains only chrom and pos, as well as rsid and sometimes effect allele, never effect + ref.
Previous solution
Fetch alleles from dbSNP REST API.
Pain points with that approach
Solution
Change dbSNP to one of our annotations, e.g. the gnomad annotation, that has alleles for a wide range of variants. We could also take allele frequencies for fin, nfsee populations to e.g. filter the hits based on whether those variants are available in the Finnish population, etc.
Steps