Genetic relationships (GRM)

This page has been last updated for R11.

Sandbox directory

Genetic relationships (GRM) are available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/grm_1.0

Data files

We use a high-quality LD-pruned subset of the imputed genotype data for genetic relationship matrix (GRM) calculation. The data has been generated using plink with hard-called genotypes. Population outliers and genetic duplicates are excluded from the imputed genotype data files and this explains the difference in samples between imputed data files and GRM files.

• R[RELEASE]_GRM_VO_LD_0.2.bed: GRM file in PLINK binary biallelic genotype table format

• R[RELEASE]_GRM VO _LD_0.2.bim: Extended variant information file accompanying the .bed file

• R[RELEASE]_GRM_VO_LD_0.2.fam: Sample information file accompanying the .bed file

• R[RELEASE]_GRM_VO_LD_0.2..log: Log from plink2

• R[RELEASE]_variants_info_allbatches_0.90.txt: Sisu v4.2 panel variants with INFO score >= 0.90 in every batch in format "ck ~_pos_ref_alt"

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