How to extract only neutral markers from low-coverage whole genome sequencing?

Question

[beausoleilmo]

I was wondering how to extract only the neutral markers from low-coverage whole genome sequencing either from a VCF file or a Beagle file. Any idea on how to do this?

Should this be done by calculating the outlier SNPs and then removing the position of the outlier from the VCF or beagle to get only neutral markers?