PLINK LD matrix determine what variants were removed

Question

[andhamel]

Hi everyone,

I am new to PLINK and trying to understand it as I go.

I currently have a list of ~6100 variants and would like to compute an LD matrix for them.

The command I launched was

plink --bfile $binary_name --keep $subset --r --matrix --extract $variant --out $output

The results were successful. The output was indeed an LD matrix.

However, the matrix was an nxn matrix of ~5900 rows, implying ~200 variants were filtered out.

Is there a way to determine which variants were removed?

Thanks in advance!

Answer 1

[chrchang523]

“plink —bfile ... —extract ... —write-snplist” should tell you what variants weren’t removed; you can then look at the difference between this and your original list.

[andhamel]

Great, thank you! Is it safe to assume that the order of the .snplist file is the same order for the LD matrix?

[chrchang523]

Yes, that’s a safe assumption.