Question: Breakdancer Bam2Cfg.Pl Does Not Produce Any Output For Treated/Tumor File
gravatar for skm770
3.6 years ago by
skm770140 wrote:


I am trying to run with two bam files one of treated sample and another of normal sample. Whenever I run the script it does not produce any info about the treated file it only produces info about the normal file in the cfg file.

This is the command line that I used.

perl /home/skhan/bio/Breakdancer/breakdancer/perl/ -g -h addRG_nanomax.bam addRG_HN002.bam > nanomax.cfg

and this is how my cfg file looks like :-

readgroup:HN002 platform:Illumina map:addRG_HN002.bam readlen:90.00 lib:LIB_HN002 num:10001 lower:409.91 upper: 535.86 mean:476.07 std:15.77 SWnormality:-56.22 flag:1(0.14%)18(96.28%)2(1.06%)20(0.01%)32(1.19%)4(1.08%)64(0.20%)8(0. 05%)20728 exe:samtools view

no information in cfg file found for nanomax.bam

I generated both the files using the same procedure of running bwa-mem and then running sortsam (picard) and addorreplacereadgroups(picard)

Following are my RG headers for both files :-

nanomax : @RG ID:nanomax PL:Illumina PU:nanomax LB:soybean_nanomax SM:nanomax CN:MU

HN002 : @RG ID:HN002 PL:Illumina PU:soy-HN002 LB:LIB_HN002 SM:soybean-HN002 CN:MU

Kindly tell me why I may be getting no information about the treated sample in the cfg file and treated file.

When I try to run only the tumor/ in my case treated file I don't get any output with bam2cfg script

breakdancer • 1.4k views
ADD COMMENTlink written 3.6 years ago by skm770140

Have you seen the previous questions about breakdancer, including this one? Empty cfg file for BreakDancer

ADD REPLYlink written 3.6 years ago by Chris Miller18k
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