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6.4 years ago
jinxinhao1988
▴
70
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?
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.