compress/recode function and missing data

[Jonathan Brassac]

Hello,

I have a vcf file that I want to compress and recode to HapMap format with blink to be used with gapit afterward. My vcf file contains missing data but when I compress/recode it, SNPs with missing genotype value for some individuals are now coded as having a genotype value in the HapMap format.

Is there any imputation done during compress/recode steps or is this an error?
Is that why we need to provide phenotypic values when recoding?
How exactly should the missing values look like in the vcf file?

Thanks,
Jonathan