to get a vairants list from GWAS catalog

[GGboy-Zzz]

Thanks you for this greate tool to access GWAS catalog datasets. I want to download the top associations SNPs from GWAS catalog, and convert it to a SNP variant list like bim file,

yet the 'get_associations' output didnt have the SNP reference allele. Can you give me some help or suggestions to extract it from GWAS catalog? I will be deeply grateful.

[ramiromagno]

Hi @GGboy-Zzz,

I am happy to help.

Can you share some sample code of what you are trying to achieve? Namely, the early steps (querying criteria) for retrieving variants?

[GGboy-Zzz]

Thank for your quickly response. I'm retrieved variants from a list of studys on relative traits, code as follows,
studies <- get_studies(efo_trait = 'melanoma') variants=get_variants(study_id='GCST000198') associations <- get_associations(study_id='GCST000198')

[ramiromagno]

Hi @GGboy-Zzz : I'm afraid the reference allele is not directly provided bythe GWAS Catalog.

[ramiromagno]

Closing due to inactivity.