Breakdancer : bam2cfg.pl doesn't work with merged bam

Question

[Rox]

Hello everyone !

I'm trying to test out Breakdancer, a tool to detect strucural variantion in a alignement ,that first require to run a perl tool which create a config file using your bam file.

I used the tool this way on a merged bam :

Loutre:~/breakdancer/perl$ ./bam2cfg.pl '/media/loutre/SUZUKII/alignement/bwamem-illumina/all-merged.bam' > configall.cfg

And so it did give some output, it seems to work

[Wed Jan 10 16:04:56 2018 ./bam2cfg.pl] Processing bam: /media/loutre/SUZUKII/alignement/bwamem-illumina/all-merged.bam
[Wed Jan 10 16:05:38 2018 ./bam2cfg.pl] selected_libs is : 1
[Wed Jan 10 16:05:38 2018 ./bam2cfg.pl] Closing BAM file
[Wed Jan 10 16:05:38 2018 ./bam2cfg.pl] Send TERM signal for 5474
[Wed Jan 10 16:05:40 2018 ./bam2cfg.pl] samtools pid process 5474 is still there...
[Wed Jan 10 16:05:40 2018 ./bam2cfg.pl] invoking kill -9 on 5474 ...
[Wed Jan 10 16:05:40 2018 ./bam2cfg.pl] Closing samtools process : 5474
Coefficient of variation 1.03635379214893 in library NA is larger than the cutoff 1, poor quality data, excluding from further analysis.

But in the end, configall.cfg is empty.

I've used the same line using only one of my merged bam file, and it worked normally. I've produce all the bam file with bwa mem alignement on several Illumina reads, that's why I'm merging in the end. There is not so much informations about this tool neither on github nor anywhere else... So I have no idea of what I did wrong. Did someone already played with this tool and can give me some enlightenments ?

Thanks for your help !

Cheers,

Roxane

Answer 1

[huirusun0305]

Hi, I have met the same problem as you have. Did you solve this problem later? I have also used the same line using only one of the input bam file of the merged one, and it worked normally. I merged the input bams and then sort and index the merged bam file. I have got error report as follows:

Processing bam /input/merge.sort.bam First read: 0 10673 Error: 1000 reads processed with no progress made. Still waiting for read groups: needs 100000 more observations Note: this limit can be adjusted by the --no-progress-count parameter.

I added --no-progress-count 20000 and tried again, but the problem has not been solved.

Looking forward to your reply~