Genotype Files in Sandbox

This page has been last updated for R11.

FinnGen updates genotype data in each Data Release and makes these files available to Sandbox users.

Sandbox directory

Genotype data is available in the following sandbox directory:

/finngen/library-red/finngen_R[RELEASE]

• Data Release 12: /finngen/library-red/finngen_R12

• Data Release 11: /finngen/library-red/finngen_R11

• Data Release 10: /finngen/library-red/finngen_R10

• Data Release 9: /finngen/library-red/finngen_R9

• Data Release 8: /finngen/library-red/finngen_R8

• Data Release 7: /finngen/library-red/finngen_R7

• Data Release 6: /finngen/library-red/finngen_R6

• Data Release 5: /finngen/library-red/finngen_R5

• Data Release 4: /finngen/library-red/finngen_R4

• Data Release 3: /finngen/library-red/finngen_R3_core_analysis_results

• Data Release 2: /finngen/library-red/finngen_R2_core_analysis_results

• Data Release 1: /finngen/library-red/finngen_R1_core_analysis_results

Data files

The data files are described in the following sections:

Imputed genotypes in VCF format

Imputed genotypes in BGEN format

Imputed genotypes in PLINK format

Chip data

Imputed HLA alleles

Principal components analysis (PCA) data

Kinship data

Analysis covariates

Polygenic risk scores (PRS)

Genetic relationships (GRM)

Mosaic chromosomal alternations (mCA)

Prune data (R9)

Imputed STR genotypes (R8)

See Release Notes to view all data releases to the Sandbox.

Data Release 12 (R12) directories

• FinnGen DF12 kinship data (version 1.0)

  • /finngen/library-red/finngen_R12/kinship_1.0/

• FinnGen DF12 pca data (version 1.0)

  • /finngen/library-red/finngen_R12/pca_1.0/

• FinnGen DF12 analysis covariates

  • /finngen/library-red/finngen_R12/analysis_covariates/

• FinnGen DF12 imputed genotype data (version 2.0)

  • /finngen/library-red/finngen_R12/genotype_1.0/

• FinnGen DF12 plink data (version 2.0)

  • /finngen/library-red/finngen_R12/genotype_plink_2.0/

• FinnGen DF12 bgen data (version 2.0)

  • /finngen/library-red/finngen_R12/bgen_2.0/

Additional notes

• FinnGen DF12 genotype data (version 1.0) has been deleted

  • /finngen/library-red/finngen_R12/genotype_1.0/

  • Please see /finngen/library-red/finngen_R12/genotype_1.0/DELETED.README

Data Release 11 (R11) directories

Imputed genotypes in VCF format

/finngen/library-red/finngen_R11/genotype_1.0/

Imputed genotypes in BGEN format

/finngen/library-red/finngen_R11/bgen/

Imputed genotypes in PLINK format

/finngen/library-red/finngen_R11/genotype_plink_1.0/

Chip data

/finngen/library-red/finngen_R11/chipd_1.0/

Imputed HLA alleles

/finngen/library-red/finngen_R11/hla_1.0/

Principal components analysis (PCA) data

/finngen/library-red/finngen_R11/pca_1.0/

Kinship data

/finngen/library-red/finngen_R11/kinship_1.0/

Analysis covariates

/finngen/library-red/finngen_R11/analysis_covariates/

Polygenic risk scores

/finngen/library-red/finngen_R11/prs_1.0/

Genetic relationships

/finngen/library-red/finngen_R11/grm_1.0/

Mosaic chromosomal alterations

/finngen/library-red/finngen_R11/mca_1.0/

List of all files in the release

/finngen/library-red/finngen_R11/catalog/catalog.txt