Observing merged genomic intervals along with their original unmerged intervals

Question

[arsala521]

Hello everyone,

Is there any option in bedtools or bedops that after merging show the original regions of the merged interval as well?

For example for the following input

chr1 500 1000
chr1 750 1000
chr2 200 500

can I have the output somewhat like this

chr1 500 1000 chr1 500 1000 chr1 750 1000
chr2 200 500

For every merged region, I want to see the original regions along with it.

Thank you

Answer 1

[Kevin Blighe]

There is definitely an awk solution here; however, you may try out BEDTools:

cat test.bed 
chr1    500 1000
chr1    750 1000
chr2    200 500

bedtools merge -i test.bed -c 1,2,3 -o distinct -delim " "
chr1    500 1000    chr1    500 750 1000
chr2    200 500     chr2    200 500

Give that a try.

Kevin