bedutils / reduce

Reduces BED regions to overlap them. The BED file *must* be sorted in order
to merge them.

Usage: bedutils reduce {opts} bedfile

-extend num{,num}   Extend the BED region {num} bases 5' and 3'
                    Can either a single number (extend the same in both
                    direction) or a comma delimited pair of numbers where the
                    first number extends the region in the 5' direction and
                    the second number extends the region in the 3' direction.

-clip               Only extend the reads to find overlapping regions, don't
                    extend the edges of the regions.

-c                  Output the number of regions merged as the score (count).
                    Otherwise, the scores for all of the regions are added

-nostrand           Ignore strand information when merging regions