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)
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