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

To learn more about the methods used, see section [GWAS](/documentation/r5/methods/phewas.md).

The `{endpoint}.gz` have the following structure:

| Column name          | Description                                                                                          |
| -------------------- | ---------------------------------------------------------------------------------------------------- |
| **`#chrom`**         | chromosome on build GRCh38 (`1-22, X`)                                                               |
| **`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)                                          |
| **`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)      |
| **`maf`**            | alternative (effect) allele frequency                                                                |
| **`maf_cases`**      | alternative (effect) allele frequency among cases                                                    |
| **`maf_controls`**   | alternative (effect) allele frequency among controls                                                 |
| **`n_hom_cases`**    | number of homozygous cases\*                                                                         |
| **`n_het_cases`**    | number of heterozygous cases\*                                                                       |
| **`n_hom_controls`** | number of homozygous 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.snp.bgz`

FINEMAP results have the following filename pattern:

* `{endpoint}.FINEMAP.region.bgz`
* `{endpoint}.FINEMAP.snp.bgz`
* `{endpoint}.FINEMAP.config.bgz`

To learn more about the methods used, see section [Fine-mapping](/documentation/r5/methods/finemapping.md).

SuSiE output files `{endpoint}.SUSIE.snp.bgz` 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) |

## LD estimation

Linkage disequilibrium (LD) was estimated from [SISU v3](/documentation/r5/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/r5/methods/genotype-imputation/ld-estimation.md).

## Variant annotation

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


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