I have a list of SNPs (in the form of a VCF) found in our [very] targeted sequencing dataset of ~15,000 individuals.
I am looking to compare the MAFs of these SNPs within this 'population' (our dataset) to their MAFs across different populations, such as the populations defined in ExAC or the 1000 Genomes Project.
Is there an effective way that you would recommend to do this?
These samples were processed using GrCh38 — I believe the ExAC variants have coordinates based on the previous build (please correct me if I'm wrong), so I'm unsure about using the MAFs from the ExAC data.
The output table I have in mind would look something like this: