I have a .vcf file with 150 000 SNPs on the X chromosome and genotypes for 5 samples from WGS.
I tried using plink. I exported the data in plink format :
vcftools --gzvcf ../rawData/FXXX_chrX_PASS_variants_hg38.vcf.gz --plink --out plink_X
Then I manually modified the .ped file so it take into account my pedigree. 3 males, 2 females. 2 cases, 3 controls. And I run the r2 function of plink.
plink --bfile plink_X --ld-xchr 1 --r2 -ld-window-kb 1 --ld-window 1000 --ld-window-r2 0 --out plink_X
The results are R2=1 everywhere no matter the size of the window.
I also tried the blocks function.
plink --bfile plink_X --ld-xchr 1 --blocks -ld-window-kb 1 --ld-window 1000 --ld-window-r2 0 --out plink_X
But no haploblocks found.
What I want is to know is the shared regions of the X chromosome for the 2 case samples. Does anyone know what I am doing wrong ? Or what else I can try ?