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Question: PLINK LD matrix determine what variants were removed
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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!

ADD COMMENTlink 9 months ago andhamel • 0 • updated 9 months ago chrchang523 5.2k
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“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.

ADD COMMENTlink 9 months ago chrchang523 5.2k
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Great, thank you! Is it safe to assume that the order of the .snplist file is the same order for the LD matrix?

ADD REPLYlink 9 months ago
andhamel
• 0
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Yes, that’s a safe assumption.

ADD REPLYlink 9 months ago
chrchang523
5.2k

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