Question about --covar-col-nums vs. PLINK 1.9's --covar-number

[Shaw Zoe]

Dear Chris Chang,

I'm a user of PLINK 2.0 and have a question about the --covar-col-nums flag. I'm trying to migrate some analyses from PLINK 1.9, and I'm a bit confused about how column numbering is handled for covariates.

In PLINK 1.9, --covar-number started counting from the first covariate column, which was typically the third column after the FID and IID columns.

Does --covar-col-nums in PLINK 2.0 work the same way, starting its count from the first covariate column, or does it count all columns starting from the FID?

For example, if my covariate file is: FID IID Age Sex PC1 Would Age be designated as column 1 or column 3 in covar-col-num?

Best

Shaw

[Chris Chang]

The flag was renamed because yes, the behavior is different from --covar-number.  "--covar-col-nums 3" is correct in your example.

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