Shapeit phasing without imputation

Question

[Sarah]

Hi everyone, I'm working with a VCF file of multiple closely related non-model species and need to phase a region of the VCF file. I would like to use Shapeit in order to use its read-backed phasing, but I would definitely not like to impute any missing genotypes. I have been able to phase the region without problem (using extractPIRs and shapeit -assemble), but is there any way to turn off the imputation behaviour, in order to not have the missing data converted to genotypes? Alternately, does anyone have a method to convert the imputed genotypes back to missing data, given a "before" and "after" VCF (ie, for a genotype that is "./." for a given site&sample in VCF #1, convert the genotype to "./." in VCF file #2)?

Thank you!