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

[ksamuk]

Hi there, you can leave missing genotypes, including sites with all missing data, in your VCF if you'd like. You can also remove sites where all individuals are missing if that is easier for you, but it should not affect the calculations.