The HLA data was imputed from R10 genotype data, using HIBAG models created by Jarmo Ritari from the Finnish Blood Bank. More information can be found in the repository:
https://github.com/FRCBS/HLA-imputation
as well as in the publication:
Ritari J, Hyvä rinen K, Clancy J, FinnGen, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a Finngen biobank cohort. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa030, https://doi.org/10.1093/nargab/lqaa030
Genotype data was constructed from the dosage data using PLINK 2.
A snp-stats report was generated with qctool
Association testing was performed using Regenie 2.2.4. Same settings were used as in the core GWAS analysis. See the Association tests page for more information.
A summary was created from the regenie summary statistic outputs. This summary contains the most significant variant (by p-value) for each phenotype. Pheweb links to phenotype and gene pages have been added as additional columns.