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:

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 inclusion and INFO score

The GWAS analysis is performed for all variants in the genotype data, and the summary statistics contain all of these variants. These results are then uploaded to the green library, and shown in pheweb. An exception to this are variants with minor allele count less than 10, which are skipped during the GWAS analysis. For some subsequent analysis such as fine-mapping, variants with INFO score lower than 0.6 are filtered out. For each release you can find the variant's INFO score, as well as other annotations, in the variant annotation file, which can be found in the green library. The path is: gs://finngen-production-library-green/finngen_R[RELEASE_NUMBER]/finngen_R[RELEASE_NUMBER]_analysis_data/annotations/

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.