Hi,
I have a single bam file that includes all mapped reads of my sample and I want to use breakdancer to find SV in comparison with my reference genome.
If I run bam2cfg.pl with my bam file, I don't get any output. Is this because breakdancer requires at least two bam files, one for my sample and one for a control, i.e. a control sample (which would be my reference genome)?
I have a single bam file that includes all mapped reads of my sample and I want to use breakdancer to find SV in comparison with my reference genome.
If I run bam2cfg.pl with my bam file, I don't get any output. Is this because breakdancer requires at least two bam files, one for my sample and one for a control, i.e. a control sample (which would be my reference genome)?
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