The LD score is defined as the sum of LD (r2 ) between a SNP and all the SNPs in a region, it reflects the linkage level of a SNP with other SNPs, higher LD score represents that this SNP is higher correlated with others. The LD scores are generally used in LD score regression to estimate the heritability of a trait or the genetic correlation between traits. To obtain the LD scores of SNPs, the individual level genotype data is required, see the following example:
./hiblup --ldscore
--bfile demo
--window-bp 1000000
--threads 10
--out test
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.
A file named “test.ldsc” will be generated in the work directory, overview of this file:
id maf ldscore M1 0.481875 1 M2 0.145 1 M3 0.320625 1 . . . . . . . . . M991 0.089375 1.044 M992 0.11375 1.33231 M993 0.31875 1.2885 M994 0.103125 1 M995 0.115625 1
As shown above, the first column is the vector of SNP names, the second is minor allele frequency, the third is the calculated LD scores.
Users can also use the publicly available LD scores file to run HIBLUP, but sometimes the column “maf” is missing. Since HIBLUP uses the “maf” column to set the options “--M” by counting the number of markers with MAF >= 0.05, thus if the option “--M” is specified when running LD score regression (e.g., the value in the file “XXX.M_5_50“), the “maf” column will be useless, users can assign any dummy values to this column.