multi-population vcf filtering for population genomics analysis

Question

[qstefano]

Hey everyone,

I'm confused about the filtering steps to apply to vcf files related to different strains of an organism.

Should I filter the vcf for MAF, missing genotypes, etc. before merging the vcf files related to the single strain? Should I perform a filtering on the single population before merging and after merging the vcf files together?

Thanks for your help