filter overlapping regions

[Pradhaun]

Hi all,

I have a file with chromosome start and stop positions (3 column file like bed file). I would like to filter overlapping positions. for eg,

chr_1 100 500
chr_1 200 650
chr_1 2200 3000
chr_1 5000 6500
chr_1 5800 7500

In the above file, I would like to remove the second and last line from the file, since it is overlapped in the previous regions. Can anybody please provide suggestions to do this?
Thanks!

[dpryan]

Using R and given a GRanges object named "bed":

 o <- findOverlaps(bed, bed)
o <- o[queryHits(o) > subjectHits(o)]
bed <- bed[-queryHits(o)]