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HIBLUP has the function of calculating LD correlation (r) for pairwise SNPs based on genotype allele counts. The commands are as follows:

./hiblup --ld
         --bfile demo 
         --window-bp 1e6
         --threads 16
         --out demo_ldm

Two files (*.info, *.bin) will be generated in the folder. Since the binary file (*.bin) cannot be opened directly, users can add a flag --write-txt in the above commands to output a readable “.txt” file.

There are several options to set the window size:

  • --window-bp: to specify the size of non-overlapped window (default 1Mb, i.e., --window-bp 1000000), in which the number of SNPs is not fixed;
  • --window-num: to specify a fixed number of SNPs in a window (e.g., --window-num 500), the size of window is not constant in this case;
  • --window-geno: to define all SNPs across entire genome as one window, note that it will take a long time and huge memory cost if there are large number of SNPs;
  • --window-file: to specify a text file in which the windows are pre-defined by users, see the file format here.