Chip data

This page has been last updated for R11.

Sandbox directory

Chip data is available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/chipd_1.0

Data files

The following files are available:

• all variants

• variants per chromosome

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

All variants

All variants are available in the following PLINK files:

data/plink/r[RELEASE]_axiom_chip_allchr.bed

data/plink/r[RELEASE]_axiom_chip_allchr.bim

data/plink/r[RELEASE]_axiom_chip_allchr.fam

data/plink/r[RELEASE]_axiom_chip_allchr.afreq

Variants per chromosome

One VCF file is available for each chromosome:

data/vcf/r[RELEASE]_axiom_chr[CHROM].vcf.gz

The VCF files come with their .tbi files.

Futher information

The chip data is comprised of multiple Affymetrix batches including samples from multiple cohorts and hospital biobanks.

Variant-wise statistics for the whole dataset are listed in the VFC INFO field.

Only the samples genotyped by the FinnGen project are included. Duplicate individuals (excluding identical twins) and biobank denials have been removed from the data. Exact details about quality control filters can be found in the readme file.

The strand (reverse/forward) varies across the variants. The strand for each variant can be found in the marker content file that can be downloaded here.

Refer to the Genotype data processing flow section for more information about chip data processing and QC.