cnv-seq reference hit

Question

[dovi]

Hi all,

I've read that CNV-seq needs a reference hit file. Is this reference file the actual reference genome (the one I used to map my reads)? Or I have to pick up one of my samples to be a reference hit file ? (I don't have "treatment/control" samples). In the case that should be the actual reference genome, how do I get the .bam file? I mean, it's the reference genome, it doesn't make sense to map it against itself.

Thanks!

Answer 1

[dovi]

So far my solution was to create a "dummy" reference sample hit that contains all positions as they also do in CNVkit when no "normal" sample is provided.