I am wondering how accurate can be the detection of SVs from breakdancer using only one bam file (no WT or Normal). I suppose that it is feasible to detect insertions deletions duplications and inversions; but what about the translocations? Running breakdancer using only one bam file, the software gave me an output containing CTX and ITX, which in my opinion we are not able to be detected without using a control sample. I mean the reads aligned against the reference genome, however before the alignment we don t know the exact genomic position that every read came from. So, even if there is a translocation, the group of reads supporting a translocation will be aligned under the correct reference genome position.
I will appreciate any useful comments on that. Thank you in advance