I am trying to filter multi-allelic sites in a VCF file to find the true multi allelic sites. Some of these have 1 read in 200, that I want to get rid of. The other alternative looks good. However, when I try to filter the alleles lower than frequency (0.05) with `vcftools` it gets rid of all variant not just the minor allele. Is there a way to filter out the minor alternate according to the frequency but not the variant completely?
Found the answer! 

 1. Convert multiallelic to biallelic vcf first
 
         bcftools norm -m - file.vcf  > biallellic.vcf
 
 2. Filter the alternative alleles under certain value

         bcftools view -e "FORMAT/AD[:1]<2 && INFO/AD[1]<5" biallelic.vcf > biallelic-filtered.vcf

 3. Convert biallelic vcf to multiallelic vcf

         bcftools norm -m + biallelic-filtered.vcf > multiallellic-filtered.vcf
    