removing overlaps from a bed file

Question

[peter]

I have a sorted bedFile with following format

chr1    982086  982105  hg19::chr1:917466..917485,-;hg_9675.1   2623    -   982092  982093  0,0,255
chr1    999312  999335  hg19::chr1:934692..934715,-;hg_9678.1   880 -   999317  999318  0,0,255

So it has nine columns. I want to merge the overlapping intervals and produce a new bed file with all of the columns as the original bed file.

I am using bedtools merge command:

bedtools mergeBed sorted.bed -c 6,7,8 -o  > nonoverlapping.bed

However, this produces an empty file. Can someone guide me how to use merge command in this case. Thanks!!!

[iraun]

Don't you need -i for the input bed file?