BreakDancer is giving blank output!

Question

[anshuman.mit]

I am not sure what I am doing wrong, but whenever I am running BreakDancer to detect translocation, I am getting a blank output. Please help me identify and fix the problem.

This is what the output of bam2cfg (filename: config_0040.cfg) looks like:

readgroup:Wk40_S08     platform:Illumnia     map:Wk40.bam     readlen:131.96     lib:S08     num:9997     lower:0.00     upper:590.70     mean:170.13     std:77.16     SWnormality:-63.17     exe:samtools view
readgroup:Wk40_S09     platform:Illumnia     map:Wk40.bam     readlen:140.85     lib:S09     num:9995     lower:0.00     upper:490.47     mean:174.70     std:62.52     SWnormality:-50.83     exe:samtools view
readgroup:Wk40_S07     platform:Illumnia     map:Wk40.bam     readlen:138.60     lib:S07     num:9992     lower:0.00     upper:584.92     mean:180.75     std:74.16     SWnormality:-60.15     exe:samtools view
readgroup:Wk40_S10     platform:Illumnia     map:Wk40.bam     readlen:131.90     lib:S10     num:9998     lower:0.00     upper:559.44     mean:164.77     std:72.51     SWnormality:-61.62     exe:samtools view
readgroup:Wk00_S04     platform:Illumnia     map:Wk00.bam     readlen:145.00     lib:S04     num:9993     lower:0.00     upper:595.78     mean:204.00     std:79.92     SWnormality:-57.13     exe:samtools view
readgroup:Wk00_S03     platform:Illumnia     map:Wk00.bam     readlen:133.13     lib:S03     num:9985     lower:0.00     upper:590.55     mean:168.25     std:73.59     SWnormality:-63.19     exe:samtools view
readgroup:Wk00_S02     platform:Illumnia     map:Wk00.bam     readlen:136.76     lib:S02     num:9985     lower:0.00     upper:527.69     mean:168.54     std:66.25     SWnormality:-60.85     exe:samtools view
readgroup:Wk00_S05     platform:Illumnia     map:Wk00.bam     readlen:137.73     lib:S05     num:9991     lower:0.00     upper:489.42     mean:166.33     std:60.46     SWnormality:-57.54     exe:samtools view

Then when I run the command below to find translocation events

perl BreakDancerMax.pl -t config_0040.cfg > tres_0040.txt

This is what the entire output file tres_0040.txt looks like (blank as in nothing below the header line #Chr1 Pos1 Orientation1 ...):

#Wk00.bam     mean:166.330     std:60.460     uppercutoff:489.420     lowercutoff:0.000     readlen:137.730     library:S05     reflen:3051413885     seqcov:0.842x     phycov:0.508x                        
#Wk00.bam     mean:204.000     std:79.920     uppercutoff:595.780     lowercutoff:0.000     readlen:145.000     library:S04     reflen:3051413885     seqcov:3.394x     phycov:2.388x                        
#Wk40.bam     mean:174.700     std:62.520     uppercutoff:490.470     lowercutoff:0.000     readlen:140.850     library:S09     reflen:3051413885     seqcov:1.141x     phycov:0.708x                        
#Wk40.bam     mean:180.750     std:74.160     uppercutoff:584.920     lowercutoff:0.000     readlen:138.600     library:S07     reflen:3051413885     seqcov:2.460x     phycov:1.604x                        
#Wk40.bam     mean:170.130     std:77.160     uppercutoff:590.700     lowercutoff:0.000     readlen:131.960     library:S08     reflen:3051413885     seqcov:0.631x     phycov:0.407x                        
#Wk00.bam     mean:168.540     std:66.250     uppercutoff:527.690     lowercutoff:0.000     readlen:136.760     library:S02     reflen:3051413885     seqcov:1.762x     phycov:1.086x                        
#Wk00.bam     mean:168.250     std:73.590     uppercutoff:590.550     lowercutoff:0.000     readlen:133.130     library:S03     reflen:3051413885     seqcov:7.067x     phycov:4.465x                        
#Wk40.bam     mean:164.770     std:72.510     uppercutoff:559.440     lowercutoff:0.000     readlen:131.900     library:S10     reflen:3051413885     seqcov:1.297x     phycov:0.810x                        
#Chr1     Pos1     Orientation1     Chr2     Pos2     Orientation2     Type     Size     Score     num_Reads     num_Reads_lib     Allele_frequency     Version     Run_Param

I tried the same for 3 other bam file pairs, and the BreakDancer output file in all cases was blank, i.e. nothing below the header line #Chr1 Pos1 Orientation1 .... So how do I fix this problem?

In case it matters, I am running BreakDancer in the Terminal of my MacBook Pro (OS X Yosemite, Version 10.10.1).

Answer 1

[ernfrid]

As far as I know the original BreakDancer perl script is unmaintained at this point. You may want to try using the latest version.

[Loveinheaven]

Hi ernfri:

When I used BreakDancer (1.4.5) for my bam file. Here's my command:

breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl -g -h MY.bam

And I only got such result:

[Thu Jan 29 07:24:47 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] Processing bam: MY.W.HQ.ST_S.bam
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] selected_libs is : 1
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] Closing BAM file
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] Send TERM signal for 52630
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] samtools pid process 52630 is still there...
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] invoking kill -9 on 52630 ...
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/bam2cfg.pl] Closing samtools process : 52630
readgroup:MY.W.All.PE    platform:NextSeq    map:MY.W.HQ.ST_S.bam    readlen:74.99    lib:MY.W.PE    num:10000    lower:0.00    upper:464.85    mean:123.74    std:74.38    SWnormality:-54.33    flag:1(0.22%)18(57.00%)2(0.03%)20(41.84%)4(0.08%)64(0.79%)8(0.03%)14384    exe:samtools view

Is there any mistake that I made?

Here I'm sure there's a inversion in the result, thought the ratio is very small (~1%-5%). Can BreakDancer find it out?

Thanks in advance!