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  • BreakDancer different results

    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 /home/taha/Softwares/breakdancer-1.1_2011_02_21/perl/Examplenew_break.cfg -c 4 -q 12 > 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 the syntax I'm using is correct? If yes, then why should be there such a difference?
    Thanks,

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