Hi There seems to be a problem with bedtools pairtobed command. I have used the following command to check whether both ends in my bedpe file overlap with bed file. my bedpe file contains 6 columns (chr,start1,end1, chr,start2,end2).However I am surprised to see the output

pairToBed -a bedpe_file -b bed_file -type both 


chr10    14400000        14440000        chr10   22040000        22080000        chr10   14400000        18240000

where 1-6 columns are from my bedpe file.