Question: Breakdancer Different Result
1
gravatar for tahamasoodi
6.0 years ago by
tahamasoodi10
tahamasoodi10 wrote:

Hi,

I'm using BreakDancer on the whole genomic data generated by Illumina Hiseq. In order to confirm that I'm running the program correctly, I tried to run it with the Yoruban genome (NA18507) which the developers have used in their algorithm. I downloaded the aligned bam file of NA18507 and used the following syntax:

./bam2cfg.pl -g -h /home/taha/Downloads/NA18507.mapped.ILLUMINA.bwa.YRI.lowcoverage.20120522.bam > Examplenewbreak.cfg

./breakdancermax -c 4 -q 12 /home/taha/Softwares/breakdancer-1.120110221/perl/Examplenewbreak.cfg > Examplenewbreak_threash.xls

However after running, I got totally different results than what authors got. I got total 7200 variants while as they got 9202+4901+665 variants.

May I know why should be there such a difference?

bioinformatics breakdancer • 1.6k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by tahamasoodi10
0
gravatar for Chris Miller
6.0 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

I imagine you're using a newer version than was used in the original paper. I believe that there have been many updates/improvements to the algorithm over the past few years.

ADD COMMENTlink written 6.0 years ago by Chris Miller20k
0
gravatar for tahamasoodi
6.0 years ago by
tahamasoodi10
tahamasoodi10 wrote:

But that does not mean that there may be difference of 8000 variants! How can I check the accuracy of BreakDancer results?

ADD COMMENTlink written 6.0 years ago by tahamasoodi10

1) You can use an orthogonal method (another algorithm)

2) For real validation of structural variants, we generally do capture, then deep sequencing of the breakpoint regions, then use an assembly-based process to confirm the presence of reads that support the breakpoint

ADD REPLYlink written 6.0 years ago by Chris Miller20k
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