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Old 04-25-2012, 08:14 PM   #1
caswater
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Default 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
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Old 07-06-2012, 06:52 AM   #2
hanifk
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I have the same problem with you, did you have fixed it?
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Old 07-13-2012, 02:36 PM   #3
tutenkhamun
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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.
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Old 07-13-2012, 03:24 PM   #4
caswater
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thank you. I haven't fixed the problem yet, but just looked at the output from Pindel now.
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Old 07-13-2012, 03:30 PM   #5
tutenkhamun
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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!
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Old 07-13-2012, 06:02 PM   #6
hanifk
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Quote:
Originally Posted by tutenkhamun View Post
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.
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Old 07-16-2012, 12:41 PM   #7
caswater
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hi hi, please kindly let me know if you could try it out--- I almost forget everything about C language -_-
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