Does it have something wrong with my Linkage Disequilibrium scatterplot?

Question

[joao_gabrielzp]

Hi everyone!

I'm doing a LD decay plot with data obtained from plink: "plink --bfile mydata --r2 --ld-window-r2 0 --ld-window 9999999 --ld-window-kb 100000 --out "r2-100000"

With the results I plotted this scatterplot:

And now I'm wondering, does this completely vertical dotted lines are normal? I've never seen anything like this on other LD scatterplots. Does this have anything to do with the fact that I'm not excluding minor allele frequencies SNPs from my analysis (MAF > 0)?

Thank you in advance.

Answer 1

[chrchang523]

Have you tried setting a minor-allele-frequency floor and seeing what happens?

(I’m making this an answer, rather than just a comment, for a reason.)

[joao_gabrielzp]

Hi chrchang523!

I have a simple question about this issue here.

I know that this occured because of some very rare alleles that are predicted to be on the same haplotype, because of a high allele resemblance, the algorythm gives them r2 = 1, but I've seen some LD plots with MAF > 0 in the literature and, apparently, nothing like this occured.

Is this a normal behavior? I work with genomic selection, and used MAF > 0.00 on all my analyses, should I exclude this messed up comparisons with MAF, exclusively for my LD decay plot?

Thanks a lot!