I have run Breakdancer on a mouse KO sample and got several lines containing intrachromosomal translocations but described as interchromosomal, i. e., CTX instead of ITX, according to breakdancer's structural variant type descriptions.
Find an example/details below.
#Command: breakdancer-max -t -q 20 -d sample.ctx -g sample_ctx_q20.bed sample_readgroup.cfg
#13-19858-SAMPLE.bam mean:311.26 std:75.69 uppercutoff:642.26 lowercutoff:34.69 readlen:95.97 library:Lib-13-19858-H1C1KO_CGATGT reflen:2661926471 seqcov:13.8981 phycov:22.5379 32:778985
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib 13-19858-SAMPLE.bam
chr10 81178302 29+12- chr10 81178677 29+12- CTX -310 99 41 13-19858-SAMPLE.bam|41
Does anyone found similar results/issues?
Thanks in advance.
This is due to supplemental alignments on the same sequence as the primary alignment sneaking in and confusing breakdancer. I just pushed a fix to github. If you grab the latest, these CTX on the same sequence calls should go away.
I've also found BreakDancer to produce yield a fair number of false positives. I think calling structural variants is just hard to do.
I don't really have a solution that I feel is a great alternative. If I recall, I think LUMPY at least yielded a reasonably sized list of candidates when I tried it, so maybe you could also try that program.