Imputed genotypes in VCF format

This page has been last updated for R11.

Sandbox directory

Imputed genotypes in the VCF format are available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/genotype_1.0

Data files

One VCF file is available for each chromosome:

data/finngen_R[RELEASE]_chr[CHROM].vcf.gz

The VCF files come with their .tbi files.

Please refer to the readme file in sandbox directory for full details of the available data.

Further information

The imputed genotype data is comprised of multiple data sets that include samples from various cohorts. The exact batches and cohorts as well as VCF INFO field tags are explained in release supplementary files. IMPUTE2 INFO metrics and allele frequencies (AF) are calculated per dataset, as well as for the entire dataset.

The data contains only variants present in the imputation panel. Chip genotype data is released separately. Duplicate individuals (excluding identical twins) and biobank denials have been removed from the data.

All variants are on the forward strand.