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2014-01-07 06:16:27 -0600 asked a question filter variant with BED file

I looked around but could not find the answer. I think this question would benefit others so I ask here. I import VCF files from whole exome and gene panel analysis. I want to "activate" variants that are within coordinates specified in a BED file and see some statistics for features in this BED file (i.e. number of variants per feature, coverage per gene). Currently the closest result I can get is the "Variant Classification Count by Gene" report. But it gives report for all genes in the gene track hence shadows the regions of my interest.

Is there a script or trick to get this done?