Last updated: 2020-05-24

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Installation

Please see the detail instructions: LD Score Regression (LDSC) https://github.com/bulik/ldsc

Download ldsc software

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

Create a conda environment with LDSC’s dependencies

You might need to update numpy (and other packages) to a newer version

conda env create --file environment.yml

Activate the conda environment with LDSC’s dependencies

conda activate ldsc

Test installation

If these commands fail with an error, then something as gone wrong during the installation process.

cd ldsc

python ./ldsc.py -h
python ./munge_sumstats.py -h

ldsc Wiki

The wiki has tutorials on estimating LD Score, heritability, genetic correlation and the LD Score regression intercept and partitioned heritability.

ldsc FAQ

Common issues are described in the FAQ


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        rprojroot_1.3-2   digest_0.6.23     later_1.0.0      
 [5] R6_2.4.1          backports_1.1.5   git2r_0.26.1.9000 magrittr_1.5     
 [9] evaluate_0.14     stringi_1.4.5     rlang_0.4.4       fs_1.3.1         
[13] promises_1.1.0    whisker_0.4       rmarkdown_2.1     tools_3.5.1      
[17] stringr_1.4.0     glue_1.3.1        httpuv_1.5.2      xfun_0.12        
[21] yaml_2.2.0        compiler_3.5.1    htmltools_0.4.0   knitr_1.28