Question: Breakdancer inaccurate output.
0
gravatar for Fernando Rossello
4.4 years ago by
Victorian Bioinformatics Consortium - Monash University
Fernando Rossello0 wrote:

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

ADD COMMENTlink modified 4.4 years ago by tgi.tabbott220 • written 4.4 years ago by Fernando Rossello0

For anyone looking for an answer the question was also asked on SEQanswers (but not answered there yet either).

ADD REPLYlink written 4.4 years ago by nnutter200

These results where observed when bwa-mem was used as aligner. I couldn't see the same type of behaviour when I used bowtie2 local. I will further investigate why this could happened.

 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Fernando Rossello0
1
gravatar for tgi.tabbott
4.4 years ago by
tgi.tabbott220
United States
tgi.tabbott220 wrote:

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.

ADD COMMENTlink written 4.4 years ago by tgi.tabbott220

Excellent! Thanks for this. I will test it and let you know if there are any issues.

Cheers,

Fernando

ADD REPLYlink written 4.4 years ago by Fernando Rossello0
1
gravatar for Charles Warden
4.4 years ago by
Charles Warden5.6k
Duarte, CA
Charles Warden5.6k wrote:

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.

ADD COMMENTlink written 4.4 years ago by Charles Warden5.6k

Yes, totally agree. Calling SVs it's just hard and complex. I am testing the same sample using LUMPY and Socrates. I will see how they compare against Breakdancer.

Cheers,

Fernando

ADD REPLYlink written 4.4 years ago by Fernando Rossello0
0
gravatar for ernfrid
4.4 years ago by
ernfrid380
Saint Louis
ernfrid380 wrote:

My best guess is that this is a bug. There are much, much newer versions of breakdancer available at this point. I would suggest trying the latest available via github (see: https://github.com/genome/breakdancer/releases).

ADD COMMENTlink written 4.4 years ago by ernfrid380

Thanks Ernfrid! Really appreciate it. I will test it and see how it goes.

Cheers,

Fernando

ADD REPLYlink written 4.4 years ago by Fernando Rossello0

Just letting you know that the latest Breakdancer version (1.4.4-unstable-9-e2ceb53) and it produces exactly the same output/bug. Will keep investigating.

Cheers,

Fernando

ADD REPLYlink written 4.4 years ago by Fernando Rossello0

Thanks Fernando. I suspect that this is an issue with BWA mem chimeric alignments. Can you post how you ran BWA mem (what command line arguments)?

ADD REPLYlink written 4.4 years ago by ernfrid380

Sure. These were the arguments (default):

bwa mem -t 12 -R "@RG\tID:$TID\tLB:$TLB\tSM:$TSM\tPL:$TPL" $bwaIndex temp1.fastq temp2.fastq > $SN

In any case, tgi.tabbott posted the reason and solution to this issue below. 

Thank you, Charles and tgi.tabbot for the help and interest.

ADD REPLYlink written 4.4 years ago by Fernando Rossello0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 828 users visited in the last hour