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?