Breakdancer number off reads
Hi, I was wondering if someone can help me out how to choose the number of read cut off. In the breakdancer output files it gives you a column with number of reads in tumor and normal sample. What is the best way to choose the number of read cut off. Can you randomly choose the cut off? The higher the number of reads the higher the specificity but the lower the sensitivity, but what number will be best. Any recommendations are welcome!
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