GWAS results format

The GWAS analysis produces the following types of files:

Summary statistics

The summary statistics are bgzipped, tabix-indexed tab separated files (.tsv). They contain the summary statistics of the GWAS analysis. The columns are the following:

Column	Description
#chrom	chromosome
pos	chromosomal position (in base pairs)
ref	reference allele
alt	alternate allele
rsids	rsIDs related to this variant
nearest_genes	nearest genes
pval	analysis p-value
mlogp	-log10(p-value)
beta	effect size of alternate allele
sebeta	standard error of effect size
af_alt	allele frequency for the alternate allele
af_alt_cases	alternate allele frequency in cases
af_alt_controls	alternate allele frequency in controls

Variant annotations and info score

The GWAS analysis is ran regardless of INFO score, and results are released into pheweb. The INFO < 0.6 is filtered out prior to certain subsequent analyses, e.g. fine-mapping. The released summary stat files contain all variants regardless of INFO score. The variant annotation file with INFO scores and other annotations can be found from the green library, e.g. for R9 gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/annotations/R9_annotated_variants_rsid_enrichment.gz

Plots

The plots produced include three types of plots: a manhattan plot of the GWAS, a manhattan plot with a log^2-scaled y-axis, and a qqplot of the GWAS.

Read more about GWAS analysis. See more information about What are QQ and Manhattan plots.