I know that using bedtools functions (specifically intersect and windows), it is possible to find overlapping features in the two sets of data. The catch here is that bedtools only accept the files in VCF, GFF, BED or BAM format. I have this tool that generates the output data in ANNOVAR format. My initial thought here is to convert the existing VCF files to ANNOVAR, but I am not sure whether there are tools out there that does the similar job as described earlier, except using the ANNOVAR files.
Thank you, Young