> For the complete documentation index, see [llms.txt](https://finngen.gitbook.io/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://finngen.gitbook.io/documentation/r6/methods/genotype-imputation/ld-estimation.md).

# LD estimation

The [BCOR](http://www.christianbenner.com/) files were created using [LDstore](http://www.christianbenner.com/) from the Finnish [SISU](/documentation/r6/methods/genotype-imputation/sisu-reference-panel.md) panel v3.

The panel has been divided per chromosome. For example, to use the LD information in the first chromosome, `FG_LD_chr1.bcor` would be the file to use.

## **Settings used**

* number of samples: 3775 
* window size: 1500 kb 
* accuracy: low 
* number of threads: 96 
* LD threshold to include correlations: 0.05

## Example usage

[LDstore v1.1](http://www.christianbenner.com/ldstore_v1.1_x86_64.tgz) can be downloaded via:

```bash
wget http://www.christianbenner.com/ldstore_v1.1_x86_64.tgz
```

And an example to extract variant range 20 Mb - 50 Mb from chromosome 7 is as follows:

```bash
ldstore --bcor FG_LD_chr7.bcor --incl-range 20000000-50000000 --table output_file_name.table
```

## Note

It is not preferred to use these LD estimate files for e.g. fine-mapping, since many of the fine-mapping methods (e.g. SuSiE) require in-sample LD information for good results!