Getting an error with ld_clump() function for variants that are in X chromosome:

[Bhashitha2014]

I am using the script as mentioned above to prune the variants that are in LD. It is working fine for the variants that are present in one of the chromosomes 1-22 but not X chromosome. While I am trying to prune the variants that are present in X chromosome, I am getting the error as mentioned below (Warning: No significant --clump results. Skipping)

but I could see variants are in LD when I ran it in the LDmatrix tool (https://ldlink.nih.gov)

Any help in this regard will be highly appreciated!!

[zyjun0216]

Hello, I also encountered this problem. Have you fixed the problem?