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!
•
written
by
andhamel •
“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.
Great, thank you! Is it safe to assume that the order of the .snplist file is the same order for the LD matrix?
Yes, that’s a safe assumption.
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