---
description: File naming pattern and file structure
---

# 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](methods/phewas).

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                                                 |

## 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`&#x20;
* `{endpoint}.SUSIE.snp.bgz`

FINEMAP results have the following filename pattern:

* `{endpoint}.FINEMAP.region.bgz`
* `{endpoint}.FINEMAP.snp.bgz`
* `{endpoint}.FINEMAP.cred.bgz` &#x20;

To learn more about the methods used, see section [fine-mapping](methods/finemapping).

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](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](methods/genotype-imputation/ld-estimation).
