Allele frequency for individuals in file

[DcornishUCL]

Hi,

Apologies if this is a silly question or has an obvious answer. I am trying to output five VCF files using bcftools filtered by a minimum minor allele frequency (minMAF) of 0.05 within specific population(s) of individuals. I run the command:

bcftools view .../ALL.chr${i}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz
-S .../${POP}file
-o ALL.chr${i}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_${POP}
-m2
-M2
-v snps
-q 0.05:minor
-O z

Does this mean that only SNPs with a minMAF of 0.05 within the individuals I specify with -S will be kept or it is minMAF across all individuals in the input VCF? Ideally, I would like to achieve the former.

Thank you and best wishes,

Dean