Post by ug96 on Mar 31, 2021 10:23:41 GMT
I am using the code segment mentioned below to identify LD friends for a list of snps. I have also added the --keep option to retain only a subset of individuals for this calculation.
--bfile 'bfile' \
--extract 'snps.txt' \
--keep 'keep.txt' \
--ld 'snps.txt' \
--ld-wind 5000 \
--ld-sig 0.05 \
However, every time I run it, I get 2 possible outputs:
- When I filter the bed file using the --extract option to retain only non-duplicated SNPs:
The output in the .r.ld file is 0 on every line and snp.ld file is NA on every single line.
- When I do not filter the bed file (no --extract option) and retain all SNPs, including duplicates:
The output in the .r.ld file is 0 on most lines except a few and snp.ld file is NA on most lines except some lines that contain some SNPs.
On further examination I noticed that all of these SNPs that are reported to be ld-friends are from the set of SNPs that are duplicated in the bfile.
I was hoping someone might have a solution to this?
Thanks in advance!