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