breakdancer - empty output?

caswater · 04-25-2012, 09:14 PM

Hi, I just ran breakDancer on a bam file. The program ran for a while, but gave out nothing in its input.

The configure file (manually configured as described on its website) is:

map:my.bam mean:334 std:44 readlen:
100.00 sample:mySample exe:samtools view

I then used the following commands to call inter-chromosomal translocation:

breakdancer_max -t -q 20 -r 10 config > result.txt

However, after several hours, the program quit without notifying anything, and the result.txt is just like:
#Software: BreakDancerMax-1.1r112
#Command: breakdancer_max -t -q 20 -r 10 config
#Library Statistics:
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib recal.bam

It didn't give any output except for the headers. Do you have any experience with it? Thank you very much

hanifk · 07-06-2012, 07:52 AM

I have the same problem with you, did you have fixed it?

tutenkhamun · 07-13-2012, 03:36 PM

The problem is because breakdancer has code from an older version of samtools. The BAM index is used for the -o option. Unfortunately, the BAM index format has changed since the last time code was copied from samtools source code into breakdancer source code. I feel this is why breakdancer crashes when run with the -o option. I don't know which version of samtools the index reading code in breakdancer corresponds to, though.

caswater · 07-13-2012, 04:24 PM

thank you. I haven't fixed the problem yet, but just looked at the output from Pindel now.

tutenkhamun · 07-13-2012, 04:30 PM

I think you will need to open up samtools.h in the breakdancer source code and compare it with bam_index.c in samtools source code. You will need to update the corresponding functions in samtools.h from bam_index.c. In the main BreakdancerMax.cpp, you will need to make sure that the functions ReadBamChr_prep and ReadBamChr work correctly with the new version of samtools. Good luck!

hanifk · 07-13-2012, 07:02 PM

Quote:

Originally Posted by tutenkhamun

I think you will need to open up samtools.h in the breakdancer source code and compare it with bam_index.c in samtools source code. You will need to update the corresponding functions in samtools.h from bam_index.c. In the main BreakdancerMax.cpp, you will need to make sure that the functions ReadBamChr_prep and ReadBamChr work correctly with the new version of samtools. Good luck!

Oh, I have been confused with this for a long time.
I will have a try as your suggestion, thank you very much.

caswater · 07-16-2012, 01:41 PM

hi hi, please kindly let me know if you could try it out--- I almost forget everything about C language -_-

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04-25-2012, 09:14 PM	#1
caswater Member Location: Canada Join Date: Jun 2011 Posts: 47	breakdancer - empty output? Hi, I just ran breakDancer on a bam file. The program ran for a while, but gave out nothing in its input. The configure file (manually configured as described on its website) is: map:my.bam mean:334 std:44 readlen: 100.00 sample:mySample exe:samtools view I then used the following commands to call inter-chromosomal translocation: breakdancer_max -t -q 20 -r 10 config > result.txt However, after several hours, the program quit without notifying anything, and the result.txt is just like: #Software: BreakDancerMax-1.1r112 #Command: breakdancer_max -t -q 20 -r 10 config #Library Statistics: #Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib recal.bam It didn't give any output except for the headers. Do you have any experience with it? Thank you very much

07-06-2012, 07:52 AM	#2
hanifk Member Location: China Join Date: Oct 2010 Posts: 18	I have the same problem with you, did you have fixed it?

07-13-2012, 03:36 PM	#3
tutenkhamun Junior Member Location: San Francisco Join Date: Jul 2012 Posts: 3	The problem is because breakdancer has code from an older version of samtools. The BAM index is used for the -o option. Unfortunately, the BAM index format has changed since the last time code was copied from samtools source code into breakdancer source code. I feel this is why breakdancer crashes when run with the -o option. I don't know which version of samtools the index reading code in breakdancer corresponds to, though.

07-13-2012, 04:24 PM	#4
caswater Member Location: Canada Join Date: Jun 2011 Posts: 47	thank you. I haven't fixed the problem yet, but just looked at the output from Pindel now.

07-13-2012, 04:30 PM	#5
tutenkhamun Junior Member Location: San Francisco Join Date: Jul 2012 Posts: 3	I think you will need to open up samtools.h in the breakdancer source code and compare it with bam_index.c in samtools source code. You will need to update the corresponding functions in samtools.h from bam_index.c. In the main BreakdancerMax.cpp, you will need to make sure that the functions ReadBamChr_prep and ReadBamChr work correctly with the new version of samtools. Good luck!

07-16-2012, 01:41 PM	#7
caswater Member Location: Canada Join Date: Jun 2011 Posts: 47	hi hi, please kindly let me know if you could try it out--- I almost forget everything about C language -_-