My VCF file is annotated with g1k frequency WHEN such a frequency is available.
I want to select all rare variants (with a frequency below a certain cutoff say 1%). Thus I want all lines where this condition is satisfied BUT I also need all the lines where there is no frequency annotation as these are also potential rare variants.
Does anyone know how to do this with bcftools expressions? I have tried but it would seem like bcftools does not provide a way of testing whether a tag is present in the INFO field.