Should sites with no depth coverage by included or excluded from VCF files while using Whole genome data for Dxy calculation?

[vincianem]

Morning,

I have a general question related to the formatting of the input VCF file for dxy and pi calculation using Pixy.

I generated VCF files from whole genome data that include invariants, variants and positions without called genotypes. I wonder if the positions without called genotypes (./.) have to be included in the VCFs for the calculations?

Thanks a lot for your answer! Best, Vinciane