breakdancer several bam misunderstand

[ralonso]

Hello,

I am calling breakdancer to see which structural variants are different from one sample to another. For these I do this two steps:
perl perl/bam2cfg.pl -g -h ivia_040_10.bam ivia_214_10.bam > both.cfg
breakdancer_max -g bed both.cfg > both.sv

My problem is that breakdancer is not reporting well the sv, for example, I see the same sv in two different lines,line 2 and 3, in the file both.sv, it just changes two bases, and if you see it in IGV, is a perfect deletion in both samples ex:

1. scaffold_1 348436 88+2- scaffold_1 349316 1+166- DEL 630 99 87 ivia_040_10.bam|84:ivia_214_10.bam|3 NA 0.30
2. scaffold_1 355952 122+0- scaffold_1 356266 1+247- DEL 329 99 122 ivia_040_10.bam|122 0.01 6.48
3. scaffold_1 355954 122+1- scaffold_1 356266 0+124- DEL 333 99 122 ivia_214_10.bam|122 NA NA
4. scaffold_1 360645 36+35- scaffold_1 361319 36+35- INS -200 99 35 ivia_040_10.bam|20:ivia_214_10.bam|15 NA NA

The thing is that some of them are well detected, like in line 1 or 4.

could anyone help me with this?

Thanks!