Multiple regression for indel data in plink

Question

[doommonk]

Hi,

I am trying to conduct a multiple regression on indel data. In my vcf file I have some variants that are biallelic and some which are multiallelic. I have already tested the biallelic data so only need to run the multiallelic.

I was given this line of code as a guide: plink --bfile mydata --linear --covar mycov.txt

I'm not sure how to lay out my covar file though or what to include in it.

Any help would be great thanks

[doommonk]

I know the covar file is meant to be formatted like:

FID    IID    COV

But should the cov be the different types of alleles or genotypes