Hello, I'm trying to extract summary information from a VCF file using VCFtools. I would like to extract this information in windows. For the nucleotide diversity I can use --window-pi and for Fst --fst-window-size. These two option give me what I need.
But, for statistics like site depth (--site-depth) I haven't been able to find an alternative to extract this information in windows.
Any suggestion on how to do it with VCFtools or with other softwares?