I have a bed file with the co-ordinates includes chr start and end columns.

 

    #chr	start	end
    chrM	1	     1
    chrM	2	     2
    chrM	3	     3
    chrM	4	     4
    chrM	5	     5
    chrM	7	     7
    chrM	8	     8
    chrM	9	     9
    chrM	10	    10
    chrM	11	    11
    chrM	12	    12
    chrM	13	    13
    chrM	14	    14
here there are 2 region are present  i want to  get output like 

    #chr    start   end
     chrM   1        5
     chrM    7       14
 which tool should i use to perform this
 after this i need to find its location into the mitochorial genome 
 I'm afraid your BED file only describes **deletions**  because a BED in half-open : see chromEnd in https://genome.ucsc.edu/FAQ/FAQformat.html#format1

the tool you need is  "bedtools merge"  http://bedtools.readthedocs.io/en/latest/content/tools/merge.html

> which tool should i use to perform this after this i need to find its location into the mitochorial genome 

uh ???