Del As Type Instead Of Ctx

Question

[lyfsa]

I am using Breakdancer to find structural variations. In the breakdancer output, sometimes type is DEL instead of CTX.. for example:

10 59991766 5+5- 11 4566490 29+29- DEL 326 99 24

10 572729 30+14- 12 37240761 14+15- DEL 224 78 8

Shouldn't the calls in different chromosome be called CTX?

[Joachim]

This question has also been asked on SourceForge (here) and SeqAnswers (here). No answers were given there, so I would suspect that you might be right, but that breakdancer is just not written that way.

[lyfsa]

I was aware that this question have been asked before. Just hoping that someone would help me find answer in this forum :)

[Joachim]

Sorry, I was not implying that you did not search the web before posting your question here. Instead, I wanted to add further emphasis to your question, because it appears to be an unsolved puzzle for quite some time now. I should have made that clearer in my first comment.

[lyfsa]

I did not mean that either..no worries :))

Answer 1

[ernfrid]

This is more than a little late in terms of response, but I thought I'd take a stab since I've been looking at BreakDancer recently.

You are correct that this shouldn't happen, but I think an edge case may occur if your BAMs have a different sort order. Can you look at the headers of your BAM files and verify that the chromosomes occur in the same order? If they do, then do you have a minimal example that you would be able to share for debugging purposes?