I have a multisample .vcf file which I've annotated with annovar (gene annotation) and I've used SnpSift CaseControl on it to assign samples as cases and controls. For each variant SnpSift reports (as extra columns in the .vcf) the number of times this variant was found in cases and in controls and it does some statistical testing. However, instead of doing this now on a variant level, I want to check if certain GENES have more variants in the controls than in the samples. This can be again an extra column in the .vcf, or something seperate. I annotated the .vcf with Annovar, so the gene information is present in the .vcf.
Is there a tool (like SnpSift) to do this? Or can I better write my own script? (if so, what would be the easiest way?)