Core analysis results files

FinnGen core analysis results files are available in the Sandbox.

Each core analysis results file is described in the following sections:

• Genotype cluster plots

• GWAS results

• Finemapping

• Colocalization

• Autoreporting data

• Sex-specific GWAS results

• Recessive GWAS results

• UKBB - FinnGen meta-analysis

• Pairwise endpoint genetic correlations

• Heritabilities

• Coding variant subset

• HLA association results

• Proteomics results

• Chip EWAS (Exome-Wide Association Scan)

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

Data freeze/Release specific analysis reports:

Analysis report R12

Analysis report R11

Analysis Report R10

Analysis Report R9

Analysis Report R8

Analysis Report R7

Analysis Report R6

Analysis Report R5

Example core analysis result files from FinnGen Release 12 (R12)

FinnGen DF12 sex-specific GWAS and heterogeneity results:

Female-/male-specific summary statistics: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/sex_difference/summary_stats/

Female-male meta-analysis summary statistics: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/sex_difference/meta_analysis/meta_summary_stats/

Aggregated meta-analysis results (all endpoints, single-sex assoc P<=5E-8): gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/sex_difference/meta_analysis/sex_specific_meta_gwsig_in_either_sex_all_endpoints.tsv.gz

FinnGen DF12 LOF results:

gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/lof/

FinnGen DF12 colocalization results data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/colocalization/ documentation: green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_colocalization.md gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_colocalization.pdf

FinnGen DF12 PRS results: gs://finngen-production-library-red/finngen_R12/prs_1.0

FinnGen DF12 conditional analysis and genetic correlation results: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/genetic_correlation/ gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/conditional_analysis/

FinnGen DF12 HLA association analysis results

data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/hla/

documentation: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_hla_analysis.md gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_hla_analysis.pdfFinnGen

R12 autoreporting & finemapping results

• finemapping data: /finngen/library-green/finngen_R12/finngen_R12_analysis_data/finemap

• autoreporting data: /finngen/library-green/finngen_R12/finngen_R12_analysis_data/autoreporting

• documentation: /finngen/library-green/finngen_R12/finngen_R12_analysis_documentation/

FinnGen R12 hla data

• /finngen/library-red/finngen_R12/hla_1.0/

FinnGen R12 meta-analysis results

• The data and documentation location in the Sandbox

• FinnGen + UKBB meta-analysis (856 binary and 10 progression endpoints):

  • gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/meta_analysis/ukbb/

FinnGen DF12 GWAS data

• data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/summary_stats

• documentation: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/

• pheweb link: https://r12.finngen.fi

FinnGen DF12 Annotation file

• Variant annotation file with INFO scores and other annotations gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/annotations/R12_annotated_variants_v1.gz

Example core analysis result files from FinnGen Release 11 (R11)

FinnGen + UKBB meta-analysis (762 endpoints) R11:

• gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/meta_analysis/ukbb/

FinnGen Release 11 coding variant association results and documentation

• The data and documentation location in the Green Library

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/coding/

FinnGen R11 HLA analysis results. The data and documentation location in the green library:

• gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/hla/

• gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/finngen_R11_hla_analysis.md

• gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/finngen_R11_hla_analysis.pdf

FinnGen Release 11 heritability and genetic correlation analysis outputs

• The data and documentation location in the green library:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/ldsc/

FinnGen Release 11 GWAS, finemapping, conditional analysis, colocalization and autoreporting data. The data and documentation location in the green library:

• GWAS:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/summary_stats

• Fine-mapping:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/finemap

• Conditional analysis:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/conditional_analysis

• Autoreporting:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/autoreporting

• Colocalization:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization

• Documentation available at:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/

• Finngen R11 cluster plot data. These data files contain genotype intensities per variant for a subset of samples that are used in cluster plots (released in the green library).

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/cluster_plot_1.0

  • Detailed paths to library red data from manifest:

    • /finngen/library-red/finngen_R11/cluster_plot_1.0/manifest.txt

• Colocalization between pQTLs and all genome wide significant hits in R10 .

  • Data location in the green library:

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/

  • The results are browsable in FinnGen browser (e.g. https://results.finngen.fi/region/H7_AMD/1:196510779-196910779, scroll down for colocalization table)

pQTL analysis and finemapping results

gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/

Example core analysis result files from FinnGen Release 10 (R10)

Colocalization between pQTLs and all genome wide significant hits in R10

gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/

• pQTL analysis and finemapping results

  • 828 and 619 samples from SomaLogic and Olink respectively samples

  • Data location in the green library:

    • gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/

• Colocalization between pQTLs and all genome wide significant hits in R10 .

  • Data location in the green library:

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/

  • The results are browsable in FinnGen browser (e.g. https://results.finngen.fi/region/H7_AMD/1:196510779-196910779, scroll down for colocalization table)
• Heritabilities and genetic correlations: /finngen/library-green/finngen_R10/finngen_R10_analysis_data/ldsc/

• Imputed HLA allele genotypes /finngen/library-red/finngen_R10/hla_1

• GWAS data location:

  • /finngen/library-green/finngen_R10/finngen_R10_analysis_data/summary_stats

  • Sex-specific association analysis results (under summary_stats)

  • Variant annotation file with INFO scores and other annotations /finngen/library-green/finngen_R10/finngen_R10_analysis_data/annotations/

• Fine-mapping data location:

  • /finngen/library-green/finngen_R10/finngen_R10_analysis_data/finemap

• Conditional analysis data location:

  • g/finngen/library-green/finngen_R10/finngen_R10_analysis_data/conditional_analysis

• Autoreporting data location:

  • /finngen/library-green/finngen_R10/finngen_R10_analysis_data/autoreporting

• Colocalization data location:

  • /finngen/library-green/finngen_R10/finngen_R10_analysis_data/colocalization

• Documentation location:

  • /finngen/library-green/finngen_R10/finngen_R10_analysis_documentation/

• FinnGen 10 HLA allele analysis results: /finngen/library-green/finngen_R10/finngen_R10_analysis_data/hla/

  • Documentation available at:

    • /finngen/library-green/finngen_R10/finngen_R10_analysis_documentation/finngen_R10_hla_analysis.pdf

• Finngen R10 cluster plot data:/finngen/library-green/finngen_R10/cluster_plots/

  • The cluster plot tsv files, that contain genotype intensities per variant for a subset of samples used in the cluster plots are released to the Sandbox at:

    /finngen/library-red/finngen_R10/cluster_plot_1.0/data/

    • Detailed paths of this data from the manifest file: /finngen/library-red/finngen_R10/cluster_plot_1.0/manifest.txt

• FinnGen R10 PRS data (version 1.0): /finngen/library-red/finngen_R10/prs_1.0/

Example core analysis result files from FinnGen Release 8 (R8)

• Genotype cluster plot file: /finngen/library-red/finngen_R8/cluster_plot_1.0/

• GWAS results: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/

• Finemapping results: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/finemap/

• Colocalization results: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/colocalization/

• Autoreporting results: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/autoreporting/

• UKBB-FinnGen meta-analysis results: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/ukbb_meta/

• All heritability estimates and genetic correlations calculated by ldsc software: /finngen/library-green/finngen_R8_analysis_data/ldsc/

• Pairwise endpoint genetic correlation format: /finngen/library-green/finngen_R8_analysis_data/ldsc/finngen_R8_FIN.ldsc.summary.tsv

• Heritabilities: /finngen/library-green/finngen_R8_analysis_data/ldsc/finngen_R8_FIN.ldsc.heritability.tsv

• Coding variant subset format:/finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/coding_variants/coding_variants.tsv.gz (all binary endpoints)

• All quantitative traits (coding variant subset): /finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/coding_variants/coding_variants.quantitative.tsv.gz

• Chip GWAS (will be released for DF9, previously was released for DF5)

• Annotation file (file including eg. counts of each variant per batch and most_severe_consequence and gene; used by finemapping pipeline and Regenie): /finngen/library-green/finngen_R8_analysis_data/annotations/

• Mapping for imputed variants: /finngen/library-green/finngen_R8_analysis_data/variant_mapping/finngen.variants.tsv

• Full dbsnp: /finngen/library-green/finngen_R8_analysis_data/variant_mapping/rsid_map.tsv

• Phenotype case/control N: finngen/library-green/finngen_R8/finngen_R8_pheno.tsv

• Release documentation: /finngen/library-green/finngen_R8/finngen_R8_analysis_documentation/

All green-library files can also be seen outside of the Sandbox, without red-data access, by using google cloud console. See instructions from here. When using google cloud console finngen/library-green/ within the above paths is replaced byproduction-library-green, otherwise the paths are the same.