Hi,

I noticed that after phasing with shapeit4, all homozygous reference sites present in my input (unphased) vcf were removed in the output vcf. Is there a way to retain these non-variable sites? I've searched the documentation but can't seem to find an option.

If not, I'm thinking to extract all the rows with . in the ALT column from the input vcf, then force all 0 / 0 calls to 0 | 0 but it seems kind of convoluted and I'm not sure how to then combine that with the phased vcf with only variable sites.

Thanks!