Question: Why my Breakdancer configure file is blank?
0
gravatar for jinxinhao1988
14 months ago by
China/Beijing
jinxinhao198860 wrote:

I am using breakdancer to call indels. After I got tumor and normal bam file. I use command line as follows to generate the cfg file. But the file is blank.

I use bwa to align reads.

$ bwa mem ref.fasta 1.fastq 2.fastq > aln_pe.sam

$ samtools view -bS aln_pe.sam > aln_pe.bam

$ perl ../../../software/breakdancer/breakdancer-1.1.2/perl/bam2cfg.pl -g -h tumor_aln.bam normal_aln.bam > glioblastoma.cfg

but the cfg file is blank. Where is the problem? should I use the sorted bam files?

snp software error • 425 views
ADD COMMENTlink written 14 months ago by jinxinhao198860

The same issue was reported a number of years ago: http://seqanswers.com/forums/showthread.php?t=33110

Please take a look to see if that thread helps.

ADD REPLYlink written 14 months ago by Kevin Blighe37k
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