creating gen file from bcftools based on minor allele frequency

Question

[switch.reem]

Dear all,

i am using impute2 for a research. i have the vcf files for which i used bcftools to generate a gen file as per the format required by impute2. is there a way that i can filter out the gen file for low allele frequency positions or even create one using bcftools from the scratch applying that filtering?