Question: Breakdancer
gravatar for sheetalshetty13
3.7 years ago by
sheetalshetty1340 wrote:

I have a config file out of Breakdancer that looks like below:

readgroup:transl_RG     platform:illumina       map:transl_RG.sorted.bam        readlen:70.00   lib:transl_RG   num:10001       lower:8.44      upper:996.38    mean:499.94     std:49.40       SWnormality:-2.61       flag:18(99.97%)32(0.03%)20006   exe:samtools view

I have put simulated translocations in the file and yet the breakdancer-max program does not identify any.

My command looks like this

breakdancer/bin/breakdancer-max -t -q 10 transl_RG.cfg >  transl_RG.ctx

Has it something to do with the flags in the config file?

Do I need reads with the unmapped flag in order for Breakdancer to detect it.

Many thanks for your time.

breakdancer • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Charles Warden4.9k • written 3.7 years ago by sheetalshetty1340
gravatar for Charles Warden
3.7 years ago by
Charles Warden4.9k
Duarte, CA
Charles Warden4.9k wrote:

I personally haven't been very satisfied by the BreakDancer result from any of the data that I have tested. However, to be fair, I have also yet to find an alternative algorithm using a similar principle that works better (I like CoNIFER for indels, but I don't have a favorite tool for translocations or inversions).

Is it possible there was a problem with your simulation? It seems like it is had to distinguish a BreakDancer problem from a simulation problem at this point.

Assuming the simulation works, how many supporting reads are there for each break point? Maybe the coverage isn't high enough?

Also, are you providing BreakDancer with normal alignments as well as translocations? I know that it crashes with HaloPlex data because that is amplicon based and the paired-ends don't have any sort of consistent insert size (so, BreakDancer doesn't return anything). So, I know for certain BreakDancer won't work if you only provide the reads from the translocation.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Charles Warden4.9k

Many thanks!!! I have only translocation reads in my file. I did not include any normal reads. I used wgsim to create fastqs and did alignment using bwa with default parameters to get bam files. However, the insert size distribution with my data shows a normal curve. I will definitely create another file with the normal reads as well and try once again. The 'translocation only' file worked perfectly with SVDetect though. Thanks once again. I will update soon.

ADD REPLYlink written 3.7 years ago by sheetalshetty1340
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