# 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](/documentation/r6/methods/phewas.md).

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 name from variant                                                                       |
| **`pval`**               | p-value from [SAIGE](https://github.com/weizhouUMICH/SAIGE)                                          |
| **`mlogp`**              | -log10(p-value)                                                                                      |
| **`beta`**               | effect size estimated with [SAIGE](https://github.com/weizhouUMICH/SAIGE) for the alternative allele |
| **`sebeta`**             | standard deviation of effect size estimated with [SAIGE](https://github.com/weizhouUMICH/SAIGE)      |
| **`af_alt`**             | alternative (effect) allele frequency                                                                |
| **`af_alt_cases`**       | alternative (effect) allele frequency among cases                                                    |
| **`af_alt_controls`**    | alternative (effect) allele frequency among controls                                                 |
| **`n_hom_cases`**        | number of homozygous cases\*                                                                         |
| **`n_hom_ref_cases`**    | number of homozygous reference cases\*                                                               |
| **`n_het_cases`**        | number of heterozygous cases\*                                                                       |
| **`n_hom_controls`**     | number of homozygous controls\*                                                                      |
| **`n_hom_ref_controls`** | number of homozygous reference controls\*                                                            |
| **`n_het_controls`**     | number of heterozygous cases\*                                                                       |

\*)Note that the results are based on imputed genotype dosages and produced using SAIGE and that is why the data is not presented as integers but might contain digits.

## 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](/documentation/r6/methods/finemapping.md).

`{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) |

`{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:

<table><thead><tr><th width="197.11655081240139">Column name</th><th>Description</th></tr></thead><tbody><tr><td><strong>Column name</strong></td><td><strong>Description</strong></td></tr><tr><td><strong>trait</strong></td><td>phenotype</td></tr><tr><td><strong>region</strong></td><td>region for which the fine-mapping was run</td></tr><tr><td><strong>h2g</strong></td><td>heritability of this region</td></tr><tr><td><strong>h2g_sd</strong></td><td>standard deviation of snp heritability of this region</td></tr><tr><td><strong>h2g_lower95</strong></td><td>lower limit of 95% CI for snp heritability</td></tr><tr><td><strong>h2g_upper95</strong></td><td><strong>upper</strong> limit of 95% CI for snp heritability</td></tr><tr><td><strong>log10bf</strong></td><td>log bayes factor compared against null (no signals in the region)</td></tr><tr><td><strong>prob_xSNP</strong></td><td>columns for probabilities of different number of independent signals</td></tr><tr><td><strong>expectedvalue</strong></td><td>expectation (average) of the number of signals</td></tr></tbody></table>

`{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 v3](/documentation/r6/methods/genotype-imputation/sisu-reference-panel.md) 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](/documentation/r6/methods/genotype-imputation/ld-estimation.md).

## Variant annotation

The variant annotation has measures (`HWE`, `INFO`, ...) listed per batch.


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