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Setting up LDSC environment

(1) Clone LDSC repository from GitHub

git clone https://github.com/bulik/ldsc.git cd ldsc

(2) Set up designated environment

wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh bash Miniconda2-latest-Linux-x86_64.sh conda env create --file environment.yml source activate ldsc

(3) Munge sum stats

  • munge_sumstats.sh

(4) Heritability

  • calculate_and_collect_h2_phase3.sh

(5) Bivariate correlations

  • calculate_and_collect_rg_phase3.sh

(6) Order of scripts (found in respective folders for KI level 1, KI level 2 and 10X genomics

  • make_gene_set_files
  • make_annotation_files
  • calculate_ld_scores
  • partition_h2

More info

For more information regarding LDSC, see the original repository.