Filter a VCF using fields stored in a different VCF

Question

[Sean]

Question:

Is there a way to filter variants in a VCF based on fields stored in a different VCF without merging the two files first?

Background:

I have a VCF file, and I would like to filter the variants by ExAC allele frequencies stored in a different VCF. I know I can use bcftools annotate to merge the allele counts from the ExAC VCF into my own VCF file and then use bcftools filter to filter by allele frequency. However, I'm wondering if there is a way to skip the merging process altogether.

I noticed that bcftools roh has an option called --AF-file which allows you to specify your frequencies in a different file. Does BCFtools or VCFtools offer a similar feature for filtering?

[Pierre Lindenbaum]

just create a filtered Exac and then only keep your variants that are present in the sub-exac ?