Hi. I'm trying to use BreakDancer tool to detect somatic SVs from my Tumor-Matched Normal cancer samples. First I produce configure files from each pair of tumor-normal BAM files and then I use breakdancer-max to produce BreakDancer output files from each configure files. But when I open the resulting BreakDancer output files, there are no reads/detection of SV from the tumor BAM file and every single read is from the normal BAM file. I tried it both with and without various [options] within the terminal command lines and everytime the result is the same, no read from the tumor BAM file. I also notice within the output file that "seqcov" and "phycov" value is 0 for the tumor BAM file while the normal BAM file has non-zero values for those tags. What am I doing wrong here? Can someone please help? Another question is what if I only use the tumor BAM file to produce configure file and BreakDancer output file? Can those reads be considered as somatic SVs or is it a must to use matched normal files?
