Breakdancer versus Pindel

[mathieu]

Hi all,

I am hesitating between Breakdancer and Pindel/Dindel for structural variation (SV) and indel detection. Does someone has ever compared or used both software? Thanks in advance for sharing your experiences!

mathieu

[Yilong Li]

I have a feeling that they would be more complementary to each other. Did you end up trying either or both and what are your experiences?

[mathieu]

I tried both and they gave quite results. Both had a main issue: what is apparently long rearrangements was treated as many short rearrangements... I put a bit this issue apart and I am not yet decided on what is the best strategy.
It is quite disappointing and I think that an effort has to be made by the community to improve the SV detection. The SNPs and indel detection has now reach a agreement point in term of algorithm (recalibration, local realignment, etc.. ), but I have the feeling that the SV detection is still very immature. And I am not even speaking with its integration with genotyping pipeline etc.

[csoong]

What did you mean by long rearrangements being treated as short ones? I thought breakdancer outputs breakpoints info not about size of rearrangements. Could you clarify? I also agree with you, SV detection is not keeping up, I think so far only the Sanger's group has a consistent way of characterizing them.

[LiLin]

Breakdancer Question

I have been calling SV by breakdancer Max (C version);
I found some warings:
1、while chr1 eq chr2,the pos2 <pos1;maybe it's a bug?
2、pos2-pos1 >100M,but the size <200bp;maybe it's rearrangement?
3、pos2-pos1 >200M,and the size >200M,and the type is DEL while the sample is blood;how about this,rearrangement too?

If you had the same question,and you have been sloved it.....Please told us your method,Thank you!

[KaiYe]

Hi all,

I am hesitating between Breakdancer and Pindel/Dindel for structural variation (SV) and indel detection. Does someone has ever compared or used both software? Thanks in advance for sharing your experiences!

mathieu

BreakDancer is a read-pair approach for SVs
Dindel is re-alignment for short indels
Pindel is split-read for both short indels and SVs

[Michael.James.Clark]

Try using them complementary to each other. If a SV has both read-pair and split-read support, it is a strong candidate.