Genome-wide LD PLINK | empty file for chromosome 24

Question

[A_Lh]

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.

[Kevin Blighe]

Which species - Bos taurus? Take a look here: https://www.cog-genomics.org/plink/1.9/input#chr_set

[A_Lh]

Yes Bos taurus. --chr-setis required only for chromosome 27, 28 and 29. My only probleme is with chromosome 24. I am working on bfiles (the same thing if I work with ped and map files).

[Kevin Blighe]

Check that no SNPs from chr24 have been filtered out based on MAF, missingness, et cetera. Also check all of the default LD flags to see which could result in nothing being called on chr24. For plink, there is also the plink2-users Google Groups: https://groups.google.com/forum/#!forum/plink2-users

Answer 1

[chrchang523]

—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.