BedOverlapName

Add overlapping bedname from second bed:

#!/bin/bash
PREFIX=$3
overlapSelect $1 $2 -mergeOutput stdout -dropped=stdout|  cut -f 1,2,3,4,8 | gawk '{OFS="\t";print $1,$2,$3,$4",'$PREFIX'"$5}'

example:

  bedOverlapName randomFeatures.bed geneAnnotation.bed EXON_  |
  bedOverlapName stdin conservedRegions.bed CR_ |
  bedOverlapName stdin UTRs UTR_

will annotate the bed names with various additional information, each seperated by a comma