I am trying to run an association analysis with plink version 1.07 using dosage files. I am working with impute2 output files but I managed to replicate the problem in a small artificial dataset.

I created a 10 individual 5 snp dataset and ran the commands

plink --fam test.fam --dosage test.dat format=3 dose1 noheader --linear --out No_covar

and

plink --fam test.fam --dosage test.dat format=3 dose1 noheader --linear --covar covar --out With_covar

I expected the second command to give me information regarding the covariates, as it does for association analysis on ped/map files. Instead, for both cases I got a file on the same form with only one line per SNP and no TEST column. Is that a plink bug? Or is it just the way covariate analysis works for dosage files?

The results I obtained were, without covariates:

SNP  A1  A2     FRQ    INFO      OR      SE       P
snp1   A   T  0.6500  1.3407  0.0000 18234.1705  0.9984
snp2   G   C  0.7500  0.6667  5.9930  1.8006    0.32
snp3   T   A  1.0000  0.0000      NA      NA      NA
snp4   T   G  1.0000  0.0000      NA      NA      NA
snp5   C   A  0.5000  2.0000  0.0000 9039.7038  0.9981

and with covariates.

SNP  A1  A2     FRQ    INFO      OR      SE       P
snp1   A   T  0.6500  1.3407  0.0000 10993.8403  0.9971
snp2   G   C  0.7500  0.6667  2.2500  1.2910  0.5299
snp3   T   A  1.0000  0.0000      NA      NA      NA
snp4   T   G  1.0000  0.0000      NA      NA      NA
snp5   C   A  0.5000  2.0000  0.0000 7709.0853  0.9978

The test.fam file:

1    1    0    0    1    1
2    2    0    0    2    1
3    3    0    0    1    1
4    4    0    0    2    1
5    5    0    0    1    1
6    6    0    0    2    2
7    7    0    0    1    2
8    8    0    0    2    2
9    9    0    0    1    2
0    0    0    0    2    2

the test.dat file

snp1 A T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0 1 0 0 1 0 0 1 0 0 0 1 0 0 1
snp2 G C 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 1 0 0
snp3 T A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
snp4 T G 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
snp5 C A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1

and the covar file

1 1 1
2 2 2
3 3 3
4 4 4
5 5 5
6 6 6
7 7 7
8 8 8
9 9 9
0 0 0