Expanding on komal.rathi's comment,

Create a BED file out of your tab file, follow the steps below:

1. Add this line: #dummy header to a new empty file
2. Use awk or cut to extract from your tab-delimited file the fields corresponding to the BED file you already have. Redirect and append (>>) the output of this command to the file created above.
3. Use bedtools intersect on the BED files that you have now.