merge structural variant calls in bedpe format

Question

[Ming Tommy Tang]

Hi all,

I have structural calls represented in bedpe format http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format

I want to merge the calls with both ends overlapping. similar to this question Merging And De-Duplicating Structural Variant Calls (Bedpe)

I also read https://groups.google.com/forum/#!topic/bedtools-discuss/JXZbJSwVxUo

and it seems to be not an easy job.

Anyone has written tools for this kind of task?

I am aware of svtools https://github.com/hall-lab/svtools, but it is still under development, and not tested yet.

Thanks!

Ming

Answer 1

[leekaiinthesky]

Does bedtools merge work for you?

http://bedtools.readthedocs.org/en/latest/content/tools/merge.html

And if not, what do you need it to do that it doesn't do? (An example might be helpful)

[Ming Tommy Tang]

bedpe1:

chr1 100 200 chr1 400 500
chr1 1000 1200 chr1 1500 1600

bedpe2

chr2 40 150   chr1 350 500
chr1 70 150  chr1 450 550

The first entry in bedpe1 overlaps with the second entry in bedpe2.

---------|---------|-----------------------|----------|-----    
-----|---------|-------------------------|---------------|---

merged to

-----|-------------|---------------------|---------------|---

This is just an example for intra-chromosomal merging.

Ideally, one can specify, how merging should be performed. minimal overlappings:

--------|------|---------------------------|-----------|-----