Hi everyone,

I am working with genome wide data (SNPs) using plink and want to compute pairwize LD  (r²)  between SNPs for each chromosome (29 chromosomes).

This is an example of script I used:

    plink --bfile myData1  --r2 --ld-window-r2 0 --out chr1 
    plink --bfile myData2  --r2 --ld-window-r2 0 --out chr2 
    .           .            .           .     .         .          
    .           .            .           .     .         .            
    .           .            .           .     .         .            
    plink --bfile myData29  --r2 --ld-window-r2 0 --out chr29

And the result  is like :
 

    CHR_A         BP_A      SNP_A  CHR_B         BP_B      SNP_B           R2
        23        10121   T2500005     23        14911   T2300007            1
        23        10121   T2500005     23        15894   T2300003    0.0175439
        23        10121   T2500005     23        43444   T2300006     0.416667
        23        10121   T2500005     23        60163   T0015398     0.416667

In fact, it works for all chromosomes  except chromosome 24, which give an embty table :

     CHR_A         BP_A      SNP_A  CHR_B         BP_B      SNP_B           R2
    

The same probleme for 3 breeds (always no results for chr24).
Do you have an idea?

Tanks for help. 

—chr-set *is* required for chromosome 24 here.  Otherwise, it is treated as chrY.

It may also affect the results for chromosome 23.  To be safe, you should always use it with nonhuman species.