Breakdancer inaccurate output.

[fjrossello]

Hi Guys,

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.

#Software: BreakDancerMax-1.1.2
#Command: breakdancer-max -t -q 20 -d sample.ctx -g sample_ctx_q20.bed sample_readgroup.cfg
#Library Statistics:
#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.

Cheers,

Fernando

[fjrossello]

Hi Guys,

For all those experiencing this issue, find the discussion and solution here.

Cheers,

Fernando