Local-covar

[Hasuni]

Hello, 

I am running a regression that uses a local-covar file. For some rows (snps), there are columns (samples) that I dont have data for so I just set those values to NA. 

When I run the regression I am getting an error that reads: "Invalid or missing token on line 1 of --glm local-covar= file". I'm assuming these are the NAs that I have in my file? If not the NAs then what else could this be? 

If NA is the issue, then what should I use for missing data. 

Hasuni

[Hasuni]

Turns out that local covar file doesnt accept NAs or periods as missing values. I was able to run successfully when I filled in missing values with random integers. 

Is there anyway to handle missing data in the local covar files?

Hasuni

[Chris Chang]

No, plink2 does not support missing data in local-covar files.  You can instead use e.g. —zero-cluster to set the corresponding genotypes to missing before running —glm.

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[Hasuni]

Ah ok, thank you. Is there anyway to add this support for local-covar files?