Imputed genotypes in BGEN format

This page has been last updated for R11.

Sandbox directory

Imputed genotypes in the BGEN format (8-bit precision) are available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/bgen

Data files

Two sets of BGEN files are available:

• variants per chromosome

• variants per chromosome chunked into smaller sets for parallel analysis (e.g. GWAS)

Both sets come with their .bgi and .sample files.

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

Variants per chromosome

One BGEN file is available for each chromosome:

data/chrom/finngen_R[RELEASE]_[CHROM].bgen

Variants per chromosome chunked into smaller sets

We usually want to have smaller files to speed up parallel analysis (e.g. GWAS). For this reason, we have chunked the data so that each file contains a fixed smaller number of variants. The number can very between releases and is available in the readme file.

Chunked BGEN files are available for each chromosome:

data/chunks/finngen_R[RELEASE]_[CHROM].[CHUNK].bgen

The [CHUNK] is an integer value that identifies each chunk for the chromosome.