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R4
R4
  • Introduction
  • Data download
  • Data description
  • Data releases
  • How to cite
  • Methods
    • Participating biobanks/cohorts
    • Genotypes
      • Genotype data
      • Genotype imputation
      • SISu reference panel
      • Software used
      • LD estimation
    • Endpoints
    • GWAS
      • Sample QC and PCA
      • Association tests
    • Fine-mapping
    • Contact
    • Github
    • FinnGen
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  1. Methods
  2. Genotypes

LD estimation

PreviousSoftware usedNextEndpoints

Last updated 5 years ago

CtrlK
  • Settings used
  • Example usage

The BCOR files were created using LDstore from the Finnish SISU 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 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