Merge overlapped gene coordinates in bed file format

Question

[mkh]

Hi

I have a bed format file which looks like this:

geneid start stop

geneA 100 250

geneA 120 320

geneA 240 600

geneB 1100 1800

geneB 1110 1600

geneB 1500 1700

and I would like to merge the overlapping intervals as follow:

geneid start stop

geneA 100 600

geneB 1100 1800

Are there any tools which I can use to merge such a file format?

Thanks

Answer 1

[Pierre Lindenbaum]

bedtools merge https://bedtools.readthedocs.io/en/latest/content/tools/merge.html