CNVs call with threshold issues

[Aimar269]

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

@etal

[etal]

I'd guess the sample is highly aneuploid and/or the signal is noisy, so the segments ended up outside the narrow window you specified with --threshold. You could try re-centering your .cns file with the --center median option, or --center-at if you know which chromosome or large segment is truly neutral -- which may be apparent if you scatter plot the segments together with SNP b-allele frequencies from a VCF.