glm on minimac3 vcf file

[Ake Lu]

Hi,

I load a vcf file output from minimac3 with format  GT:DS:GP and I'd like to run glm based on the dosage (dosage=DS). I just tried the glm command as the following

>pseq proj glm --phenotype myphenotype

VAR     REF     ALT     N       F       BETA    SE      STAT    P

chr5:11982      G       C       2329    0.000214684     4.8903  4.74749 1.03008 0.303079

chr5:12009      G       C       2329    0.000214684     3.0337  4.74815 0.638923        0.522936

chr5:12041      A       T       2329    0.733577        -0.12438        0.157209        -0.791177       0.428921

chr5:12072      G       C       2329    0       0       NA      NA      NA

chr5:12142      T       G       2329    0       0       NA      NA      NA

chr5:12180      T       G       2329    0.00601116      -1.46051        0.902137        -1.61894        0.105595

But I am not sure which genotype format was used under pseq glm. Is there any way to specify using "DS"?

Thanks!

Ake