FinnGen Handbook

FinnGen Handbook

Introduction
Where to begin
Background Concepts
FinnGen Data Specifics
Disease Specific Task Forces
Working in the Sandbox
Working outside the Sandbox
FAQ
Release Notes
Tool Catalog
Glossary
User Support
Data Protection & Security

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Sandbox directory
Data files
Further information

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FinnGen Data Specifics

Red Library Data (individual level data)

Genotype data

Genotype Files in Sandbox

Imputed HLA alleles

PreviousChip data NextPrincipal components analysis (PCA) data

Last updated 6 months ago

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This page has been last updated for R11.

Sandbox directory

HLA alleles (short tandem repeat) genotypes are available in the following sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/hla_1.0/

Data files

R[RELEASE]_HLA.bgen: HLA allele genotype data in bgen format
R[RELEASE]_HLA.bgen.bgi: HLA allele genotype index in bgen format
R[RELEASE]_HLA.bgen.sample: HLA allele genotype sample file
R[RELEASE]_HLA.bgen.snpstats: HLA allele snpstats file
dosage/[GENE].dosage: Dosage dta for a single gene
dosage/[GENE].dosage.map: Dosage mapping file

Data is available for the following HLA genes: A, B, C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5.

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

Further information

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HLA imputation method