Does anyone know existing pipelines to evaluate SV/CNV calling tools.
Suppose I have a BED file with the ground truth for simulated SVs, and BED files with results for different tools.
Which measures do people use to compare the performance of such tools?
I know that some people use "touch" (considering at least 1 base of overlap), or "percentage" (taking into account a threshold percentage to consider a hit) to calculate concordance, precision, etc.
Are there other measures or tools you guys are aware of?
Thanks in advance.