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?