# Data description ## Summary association statistics GWAS summary statistics (tab-delimited, bgzipped, genome build 38, [tabix](https://github.com/samtools/htslib) 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](https://finngen.gitbook.io/documentation/r9/methods/phewas). The `{endpoint}.gz` have the following structure: | 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](https://github.com/FINNGEN/regenie) | | **`mlogp`** | -log10(p-value) | | **`beta`** | effect size (log(OR) scale) estimated with [regenie](https://github.com/FINNGEN/regenie) for the alternative allele | | **`sebeta`** | standard error of effect size estimated with [regenie](https://github.com/FINNGEN/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 | ## Fine-mapping results Two fine-mapping methods were used: * [SuSiE](https://stephenslab.github.io/susie-paper/index.html) * [FINEMAP](http://www.christianbenner.com) 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](https://finngen.gitbook.io/documentation/r9/methods/finemapping). `{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: | Column name | Description | | --------------- | ---------------------------------------------------------------------------------------------------------------- | | **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 | `{endpoint}.SUSIE.snp.bgz` contain variant summaries with credible set information and have the following structure: | **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) | `{endpoint}.FINEMAP.config.bgz` contain summary fine-mapping variant configurations from FINEMAP method and have the following structure: | Column name | Description | | ----------------- | --------------------------------------------------------------------------- | | **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 | `{endpoint}.FINEMAP.region.bgz` contain summary statistics on number of independent signals in each region and have the following structure:
Column nameDescription
Column nameDescription
traitphenotype
regionregion for which the fine-mapping was run
h2gheritability of this region
h2g_sdstandard deviation of snp heritability of this region
h2g_lower95lower limit of 95% CI for snp heritability
h2g_upper95upper limit of 95% CI for snp heritability
log10bflog bayes factor compared against null (no signals in the region)
prob_xSNPcolumns for probabilities of different number of independent signals
expectedvalueexpectation (average) of the number of signals
`{endpoint}.FINEMAP.snp.bgz` has summary statistics of variants and into what credible set they may belong to. Columns: | Column name | Description | | --------------- | --------------------------------------------------------------------------- | | **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 | ## LD estimation Linkage disequilibrium (LD) was estimated from [SISU v4](https://finngen.gitbook.io/documentation/r9/methods/genotype-imputation/sisu-reference-panel) for each chromosome. Use the tool [LDstore (v1.1)](http://www.christianbenner.com/ldstore_v1.1_x86_64.tgz) for further usage of the bcor files. `ldstore --bcor FG_LD_chr1.bcor --incl-range 20000000-50000000 --table output_file_name.table` To learn more about the methods used, see section [LD estimation](https://finngen.gitbook.io/documentation/r9/methods/genotype-imputation/ld-estimation). ## Variant annotation The variant annotation has measures (`HWE`, `INFO`, ...) listed per batch.