Is There A Tool That Would Directly Encode Minor Alllele Freq In The Info Column Of A Vcf?

Question

[rickyflintoff]

Is there a tool that would directly encode minor alllele freq in the INFO column of a VCF? Or write the minor allele frequency to a given file with chrom pos pair?

[NB]

you wanted to calculate the frequency against 1000genomes/hapmap/dbsnp or ...?
you can write a script to calculate the frequency by using the info, if available, in your vcf file; by dividing AN (allele number) by AC (allele count)

[Alex Paciorkowski]

I think the OP wants a tool that will pull the MAFs from dbSNP for each rs, which on first pass might be useful for filtering. If so, use this with caution as many disease-causing alleles are nevertheless in dbSNP. AFAIK, neither of the 2 tools I am most familiar with for vcf annotation (annovar and SeattleSeq) proviide MAF values, and the reason is probably that information is not as useful as it appears to be at first. See http://www.openbioinformatics.org/annovar/annovar_filter.html#dbsnp for a discussion.