Biostar Beta. Not for public use.
all the SV type of breakdancer output are ITX is that correct?
0
Entering edit mode
4.4 years ago
jmche • 0
Korea, Republic Of

I am very confused that the output of breakdancer's(1.4.5) SV type are only ITX, I saw someother's question nobody 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)

ADD COMMENTlink
0
Entering edit mode
10 months ago
Chirag Nepal ♦ 2.2k
Copenhagen

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

ADD COMMENTlink
0
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode
3.2 years ago
ernfrid • 200
United States

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.

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1