<![CDATA[BOL: Why BreakDancer does not displays the amount of reads supporting SV?]]> https://bioinformaticsonline.com/answers/view/30107/why-breakdancer-does-not-displays-the-amount-of-reads-supporting-sv? https://bioinformaticsonline.com/answers/view/30107/why-breakdancer-does-not-displays-the-amount-of-reads-supporting-sv Sat, 10 Dec 2016 16:44:38 -0600 https://bioinformaticsonline.com/answers/view/30107/why-breakdancer-does-not-displays-the-amount-of-reads-supporting-sv <![CDATA[Why BreakDancer does not displays the amount of reads supporting SV?]]> Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Using following commands:

bam2cfg.pl -g -h dis.bam normal.bam > config_file.cfg
breakdancer_max -d test config_file.cfg > dis_normal.ctx

the 11th output column should displays the amount of reads supporting the called SV per bam-file. I have some unusual research in 11th column, can you please helpme to fix it.


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