Autoreporting results format
The autoreporting files consist of two file types: variant and group reports.
Autoreporting outputs two types of tab-separated results: variant and group reports. Group reports contain information about the groups built around credible sets, with one credible set per row. They have information about the credible set, and are annotated with various annotations.
The variant reports list all of the variants in the group reports' groups. These variants include credible set variants, as well as variants that were LD clumped together witrh the group lead variant. These are also annotated using a set of annotations. For more information about the Autoreporting tool and how it works, see Autoreporting in FinnGen.
Group reports
The columns are:
phenotype
Phenotype description
phenotype_abbreviation
Phenotype name
locus_id
Locus id (credible set max PIP variant), formatted as: chrCHROM_POS_REF_ALT
rsids
rsids matching lead variant
Cases
\# of cases in phenotype
Controls
\# of controls in phenotype
chrom
chromosome
pos
position of lead variant
ref
ref allele of lead variant
alt
alt allele of lead variant
pval
p-value of lead variant
lead_r2_threshold
r2 threshold used for LD clumping variants to lead variant.
lead_beta_previous_release
lead variant effect size in previous release
lead_pval_previous_release
lead variant p-value in previous release
lead_most_severe_consequence
lead variant most severe consequence. Taken from finngen variant annotation
lead_most_severe_gene
lead variant gene of the most severe consequence. Taken from finngen variant annotation
lead_mlogp
lead pval, transformed to -log10(pval)
lead_beta
lead effect size
lead_sebeta
lead std error of effect
lead_af_alt
lead alt allele frequency
lead_af_alt_cases
lead alt allele frequency for cases
lead_af_alt_controls
lead alt allele frequency for controls
gnomAD_functional_category
if lead variant had a functional effect (LoF,pLoF etc.), it is reported here.
gnomAD_enrichment_nfsee
lead variant Finnish enrichment against non-Finnish, non-Swedish, non-Estonian European population. from gnomAD 2.1 exome data.
gnomAD_fin.AF
Finnish AF in gnomAD 2.1 exome data
gnomAD_fin.AN
finnish allele number in gnomAD 2.1 exome data
gnomAD_fin.AC
Finnish allele count in gnomAD 2.1 exome data
gnomAD_fin.homozygote_count
Finnish homozygote count in gnomAD 2.1 exome data
gnomAD_fet_nfsee.odds_ratio
Fischer's exact test for enrichment odds ratio in Finnish vs non-Finnish, non-Estonian, non-Swedish European population. from gnomAD 2.1 exome data.
gnomAD_fet_nfsee.p_value
Fischer's exact test for enrichment p-value in Finnish vs non-Finnish, non-Estonian, non-Swedish European population. from gnomAD 2.1 exome data.
gnomad_nfsee.AC
gnomAD 2.1 non-Finnish,-Swedish,-Estonian European population allele frequency
gnomAD_nfsee.AN
gnomAD 2.1 non-Finnish,-Swedish,-Estonian European population allele frequency
gnomAD_nfsee.AF
gnomAD 2.1 non-Finnish,-Swedish,-Estonian European population allele frequency
cs_id
credible set identifier
cs_size
credible set size
cs_log_bayes_factor
credible set lgo10 bayes factor
cs_number
credible set number
cs_region
Genomic region that was fine-mapped
good_cs
see finemapping documentation
credible_set_min_r2_value
minimum r2 to max PIP variant in credible set
start
first variant in group (credible set + LD partners)
end
last variant in group
found_associations_strict
Associations credible set variants have in GWAS catalog. Associations are in format ASSOCIATION_NAME|r2_to_lead;ASSOCIATION_NAME|r2_to_lead
found_associations_relaxed
Associations group variants have in GWAS catalog. Associations are in format ASSOCIATION_NAME|r2_to_lead;ASSOCIATION_NAME|r2_to_lead
specific_yefo_trait_associations_strict
Associations credible set variants have in GWAS catalog. If the endpoint was matched to any specific EFO codes beforehand, those associations will show here. Associations are in format ASSOCIATION_NAME|r2_to_lead;ASSOCIATION_NAME|r2_to_lead
specific_efo_trait_associations_relaxed
Associations group variants have in GWAS catalog. If the endpoint was matched to any specific EFO codes beforehand, those associations will show here.Associations are in format ASSOCIATION_NAME|r2_to_lead;ASSOCIATION_NAME|r2_to_lead
n_ld_partners_0_8
amount of LD partners with r2 > 0.8
n_ld_partners_0_6
amount of LD partners with r2 > 0.6
The variant reports contain
credible set variants
annotated using summary statistics
FinnGen
assorted additional annotations
are compared against the GWAS catalog
They are TSV files and contain one row per variant.
The group reports contain formation per credible set. They are aggregated from the variant reports, with one credible set per row.
For more information, see the release documentation:
/library-green/finngen_R8_analysis_documentation/
Columns can and do vary between releases.
The HGNC symbols in the autoreporting files are version 38, as well as the VEP cache. "The most_severe_gene" and "most_severe" columns in the autoreporting file come from the finngen annotation file. Analysis team will update the release documentation to include this information (including those versions) for future releases.
Read more about Autoreporting in FinnGen, and see also FAQ Do the autoreports report the 95% or 99% credible sets
Last updated