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!