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.low_coverage.20120522.bam > Examplenew_break.cfg
./breakdancer_max -c 4 -q 12 /home/taha/Softwares/breakdancer-1.1_2011_02_21/perl/Examplenew_break.cfg > Examplenew_break_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?
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tahamasoodi •
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.
But that does not mean that there may be difference of 8000 variants! How can I check the accuracy of BreakDancer results?
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
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