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 !