Hi everyone, I've runned cnvkit.py call by using --threshold=-0.20,0.20. It gives me as result on copy number column (cn) : 0 -1 and 3 (Loss and Gain) I do not have any Neutral copy in my results. (I'm using Linux Ubuntu)

cnvkit.py call "$SAMPLE_DIR/${SAMPLE}.cns" --threshold=-0.20,0.20 \
 -o "$SAMPLE_DIR/${SAMPLE}.called.cns"

So normally, according to my threshold and the log2 values I've, I should have some Neutral CNVs in my results.

If anyone can help me on this problem;; it could be helpfull. Thanks