File naming pattern and file structure
GWAS summary statistics (tab-delimited, bgzipped, genome build 38, tabix index files included) are named as {endpoint}.gz. For example, endpoint I9_CHD has I9_CHD.gz and I9_CHD.gz.tbi.
To learn more about the methods used, see section GWAS.
The {endpoint}.gz have the following structure:
Two fine-mapping methods were used:
Fine-mapping results are tab-delimited and bgzipped.
SuSiE results have the following filename pattern:
{endpoint}.SUSIE.cred.bgz
{endpoint}.SUSIE.cred_99.bgz
{endpoint}.SUSIE.snp.bgz
FINEMAP results have the following filename pattern:
{endpoint}.FINEMAP.config.bgz
{endpoint}.FINEMAP.region.bgz
{endpoint}.FINEMAP.snp.bgz
To learn more about the methods used, see section Fine-mapping.
{endpoint}.SUSIE.cred.bgz contain credible set summaries from SuSiE fine-mapping for all genome-wide significant regions. {endpoint}.SUSIE.cred_99.bgz contain the 99% credible set summaries while the default is 95%. They have the following structure:
{endpoint}.SUSIE.snp.bgz contain variant summaries with credible set information and have the following structure:
{endpoint}.FINEMAP.config.bgz contain summary fine-mapping variant configurations from FINEMAP method and have the following structure:
{endpoint}.FINEMAP.region.bgz contain summary statistics on number of independent signals in each region and have the following structure:
{endpoint}.FINEMAP.snp.bgz has summary statistics of variants and into what credible set they may belong to. Columns:
The variant annotation has measures (HWE, INFO, ...) listed per batch.
Loss of function (LoF) variants were generated from vcf files with VEP (https://github.com/Ensembl/ensembl-vep). LoF variants are defined as having consequences in the list [frameshift_variant,splice_donor_variant,stop_gained,splice_acceptor_variant]. Also, a max_maf (0.01) and minimum info score (0.8) filters are applied. Then a bgen file is formed by filtering chromosome based vcfs and merging them into a single file, allowing us to run the whole analysis in one data set. Then the bgen is passed to step 2 of regenie in burden mode, which uses the nulls from the standard GWAS runs.
## File structure
### Data
| File | Description |
|---|---|
|finngen_R8_lof_txt.gz | Merged results, sorted by mglop. |
|finngen_R8_lof_variants.txt | A tsv file with variant/geno/lof data used in the run. |
|finngen_R8_lof_sig_hits.txt | A summary of the results only including hits for mlogp > 3 and sorted by difference between mlogp and max(mlogp) of its variants.|
### Documentation
| File | Description |
|---|---|
|finngen_R8_lof.log| Merged logs of all runs.|
| Column name | Description |
|---|---|
| Column name | Description |
|---|---|
| Column name | Description |
|---|---|
| Column name | Description |
|---|---|
Column name
Description
#chrom
chromosome on build GRCh38 (1-23)
pos
position in base pairs on build GRCh38
ref
reference allele
alt
alternative allele (effect allele)
rsids
variant identifier
nearest_genes
nearest gene(s) (comma separated) from variant
pval
p-value from regenie
mlogp
-log10(p-value)
beta
effect size (log(OR) scale) estimated with regenie for the alternative allele
sebeta
standard error of effect size estimated with regenie
af_alt
alternative (effect) allele frequency
af_alt_cases
alternative (effect) allele frequency among cases
af_alt_controls
alternative (effect) allele frequency among controls
Column name
Description
trait
phenotype
region
region for which the fine-mapping was run
cs
running number for independent credible sets in a region
cs_log10bf
Log10 bayes factor of comparing the solution of this model (cs independent credible sets) to cs -1 credible sets
cs_avg_r2
Average correlation R2 between variants in the credible set
cs_min_r2
minimum r2 between variants in the credible set
low_purity
cs_size
how many snps does this credible set contain
Column name
Description
trait
endpoint name
region
chr:start-end
v
variant identifier
rsid
rs variant identifier
chromosome
chromosome on build GRCh38 (1-22, X)
position
position in base pairs on build GRCh38
allele1
reference allele
allele2
alternative allele (effect allele)
maf
minor allele frequency
beta
effect size GWAS
se
standard error GWAS
p
p-value GWAS
mean
posterior expectation of true effect size
sd
posterior standard deviation of true effect size
prob
posterior probability of association
cs
identifier of 95% credible set (-1 = variant is not part of credible set)
lead_r2
r2 value to a lead variant (the one with maximum PIP) in a credible set
alphax
posterior inclusion probability for the x-th single effect (x := 1..L where L is the number of single effects (causal variants) specified; default: L = 10)
Column name
Description
trait
phenotype
region
region for which the fine-mapping was run
rank
rank of this configuration within a region
config
causal variants in this configuration
prob
probability across all n independent signal configurations
log10bf
log10 bayes factor for this configuration
odds
odds of this configuration
k
how many independent signals in this configuration
prob_norm_k
probability of this configuration within k independent signals solution
h2
snp heritability of this solution
h2_0.95CI
95% confidence interval limits of snp heritability of this solution
mean
marginalized shrinkage estimates of the posterior effect size mean
sd
marginalized shrinkage estimates of the posterior effect standard deviation
Column name
Description
trait
phenotype
region
region for which the fine-mapping was run
h2g
heritability of this region
h2g_sd
standard deviation of snp heritability of this region
h2g_lower95
lower limit of 95% CI for snp heritability
h2g_upper95
upper limit of 95% CI for snp heritability
log10bf
log bayes factor compared against null (no signals in the region)
prob_xSNP
columns for probabilities of different number of independent signals
expectedvalue
expectation (average) of the number of signals
Column name
Description
trait
phenotype
region
region for which the fine-mapping was run
v
variant
index
running index
rsid
rs variant identifier
chromosome
chromosome
position
position
allele1
reference allele
allele2
alternative allele
maf
alternative allele frequency
beta
original marginal effect size
se
original standard error
z
original zscore
prob
post inclusion probability
log10bf
log10 bayes factor
mean
marginalized shrinkage estimates of the posterior effect size mean
sd
marginalized shrinkage estimates of the posterior effect standard deviation
mean_incl
conditional estimates of the posterior effect size mean
sd_incl
conditional estimates of the posterior effect size standard deviation
p
original p-value
csx
credible set index for given number of causal variants x