For CNV detection from targeted NGS data, I'm running the ExomeDepth tutorial, but in the step of building the most appropriate reference set as following:
my.choice <- select.reference.set (test.counts = my.test,reference.counts = my.reference.set, bin.length = (my.counts.dafr$end - my.counts.dafr$start))
I received the following errors:
Optimization of the choice of aggregate reference set, this process can take some time It looks like the test samples has only 0 bins with 2 or more reads. The coverage is too small to perform any meaningful inference so no likelihood will be computed.
Any recommendation, please? Thanks for your help.