LD estimation

The BCOR files were created using LDstore from the Finnish SISu panel v4.2.

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 can be downloaded via:

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:

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!

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