Hello,

In my analytic workflow that is assessing GxE interaction using WGS Trio data, I have a step that calculates the minor allele frequency based on the parental genotypes. I am using VCFTools to do so, but was just wondering if the order of the flags mattered here.

For instance, If I switch the --keep and --freq flags, does it change which dataset the MAF is being calculated on? Does dropping all non-parent samples make it so the MAF is only determined on the parents?

vcftools 
--vcf input.vcf
--keep parents.txt 
--freq 
--out mafcol.txt

Thank you!