Using bedtools, create a new bed file which is the union of multiple bed files. Takes as input a file containing a list of bed files.

union_bed.sh

#!/bin/bash

cat $1 | while read f;
do
cat $f >> fullbed.bed
done

sort -k1,1 -k2,2n fullbed.bed > fullbed.sorted.bed
rm fullbed.bed
bedtools merge -i fullbed.sorted.bed > merged_bed_union.bed
rm fullbed.sorted.bed