all the SV type of breakdancer output are ITX is that correct?

Question

[jmche]

I am very confused that the output of breakdancer's(1.4.5) SV type are only ITX, I saw some other questions, nobody's is like mine.

Output:

#Chr1    Pos1    Orientation1    Chr2    Pos2    Orientation2    Type    Size    Score    num_Reads    num_Reads_lib    01.AGS.bam
chrM    78    9+7-    chrM    196    9+7-    ITX    -100    99    7    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|7    NA
chrM    333    4+4-    chrM    386    4+4-    ITX    -104    86    4    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|4    NA
chrM    830    4+4-    chrM    904    4+4-    ITX    -108    79    4    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|4    NA
chrM    970    2+2-    chrM    999    2+2-    ITX    -98    55    2    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|2    NA
chrM    1185    2+2-    chrM    1222    2+2-    ITX    -97    52    2    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|2    NA
chrM    1343    7+6-    chrM    1483    7+6-    ITX    -106    99    6    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|6    NA
chrM    1563    4+4-    chrM    1599    4+4-    ITX    -106    94    4    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|4    NA
chrM    2061    2+2-    chrM    2116    2+2-    ITX    -99    47    2    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|2    NA
chrM    2355    2+2-    chrM    2379    2+2-    ITX    -113    57    2    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|2    NA
chrM    2550    29+27-    chrM    2962    29+27-    ITX    -106    99    27    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|27    NA
chrM    3026    6+6-    chrM    3200    6+6-    ITX    -100    93    6    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|6    NA
chrM    3278    3+3-    chrM    3307    3+3-    ITX    -111    76    3    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|3    NA
chrM    3544    6+6-    chrM    3677    6+6-    ITX    -115    99    6    /isilon/jmche/ExomeSeq/bam_fixRG_1/01.AGS.bam|6    NA

And I tried several times like below, however all the output just had ITX type, no DEL INV or INS

A)

perl bam2cfg.pl -g sample1.bam > sample1.cfg
breakdancer_max -s 7 -c 3 -m 1000000000 -q 35 -r 2 -x 1000 -b 100 -y 30 sample1.cfg > sample1.ctx

B)

perl bam2cfg.pl -g sample1.bam  normal.bam > two.cfg
breakdancer_max -s 7 -c 3 -m 1000000000 -q 35 -r 2 -x 1000 -b 100 -y 30 two.cfg > two.ctx

C)

perl bam2cfg.pl -g sample1.bam  sample2.bam sample3.bam sample4.bam sample5.bam > five.cfg
breakdancer_max -s 7 -c 3 -m 1000000000 -q 35 -r 2 -x 1000 -b 100 -y 30 five.cfg > five.ctx

Is there anyone know what's is wrong?

And I also want to know if breakdancer can just suitble to tumor and normal paired data? or use it just like what I did code C since I have seen someother use it like this. Also I would be very appreciate that if tell me what is the different between single sample run and multiple samples (run code A five time VS code C at one time)

Answer 1

[Chirag Nepal]

I think you should do like B), give tumor and normal pair for each patient.

[jmche]

Thanks for your reply, however could tell me why the SV type only has ITX type? I am not only test on one sample I tried lots of samples(WES and also WGS data) and all of them just have ITX.

PS: I dont have the normal sample so I change the name of one sample to normal and assume it is the normal sample when I try code B).

I really confused and need your help. Thanks

Answer 2

[ernfrid]

Breakdancer will call ITX if the read pairs are everted. Is this a standard Illumina library? I assume it most likely is, but mate-pair libraries are not supported with 1.4.5. Even with standard libraries, if the insert size is small the reads tend to get clipped and result in read pairs that show this signal. The same is true for processing where adapter clipping is undertaken.

My recommendation would be to try a different SV caller. I would highly recommend LUMPY.