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).
Hi ernfri:
When I used BreakDancer (1.4.5) for my bam file. Here's my command:
And I only got such result:
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!