Partitioned LD Scores for the EAS population

The aim of this repository is to provide a pre-computed partitioned LD Score for the EAS population, which is used in the ldsc partitioning heritability analysis.

The files are yet incomplete and still undergoes a validation process.

Requirements

These requirements are only for those who want to reproduce our calculations. You can use our pre-computed partitioned LD scores by just downloading them from the release page.

• Python
• GNU Parallel (to be replaced)
• ldsc

Python packages

• numpy
• pandas
• bx-python

Datasets

• The 1000 Genomes Projects Phase 3 (version 5a) dataset

  • The original .vcf files were retrieved from their ftp site.
  • We then converted them to appropriate PLINK .bed format by using convert2plink.sh.
  • All PLINK files are provided as 1000G_plinkfiles_EAS.tar.gz. Users do not have to download the original 1000 Genomes Project dataset.

• The original .bed files for annotation provided by the authors.

  • Please retrieve them from here, and place them appropriately.
  • The .bed files for baseline is baseline_bedfiles.tgz, and for cell-type/cell-type-group specific annotation is ct_and_ctg_bedfiles.tgz.
  • Then, edit the scripts to set the path to these files.

Usage

You can download our pre-computed partitioned LD scores for the EAS population from here. More detailed usage of those files can be found at the original ldsc wiki.

For those who want to replicate our calculations, you can run the following command for e.g. baseline annotations.

mkdir baseline && cd $_
for chr in $(seq 22); do
    ../baseline.sh ../1000G_plinkfiles_EAS/1000G.mac5asn.$chr
done

Acknowledgements

• The ldsc was developed by Brendan Bulik-Sullivan and Hilary Finucane. The original .bed files for the categories were provided by the authors and retrieved from here.
  • Bulik-Sullivan, B. K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291–295 (2015). doi:10.1038/ng.3211.
  • Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228–1235 (2015). doi:10.1038/ng.3404.
• chromtree.py was written by Kamil Slowikowski.

Contact

Masahiro Kanai

• masahiro.kanai@riken.jp
• http://mkanai.github.io/