Bedtools intersect with index

Question

[landscape95]

Hello everyone, I wonder are there any ways that bedtools intersect can display index of the matched pairs. For example: a.bed

chr1 10 20

chr1 30 40

chr1 50 80

b.bed

chr1 12 15

chr1 16 19

chr1 22 27

chr1 31 37

The results:

chr1 10 20 chr1 12 15 1 <- here is the index of the corresponding line index in b.bed file

chr1 10 20 chr1 16 19 2

chr1 30 40 chr1 31 37 4

Your help is really appreciated!

Answer 1

[Alex Reynolds]

Via BEDOPS bedmap:

$ bedmap --echo --echo-map --delim '\t' a.bed <(awk '{ print $0"\t"NR }' b.bed) > answer.bed

Just make sure your BED files are sorted per BEDOPS sort-bed. Hope this helps!