Hi everyone, hope eveeything is going well.

I'm currently using CNVKit with the call command to call CNVs by using a specific threshold. I've find this a weird result that is identified as a loss and according to the result it should be a Neutral result.

So if anyone here have a idea, it could be helpfull.

Here the command I've used :

 if ! cnvkit.py call "$SAMPLE_DIR/${SAMPLE}.cns" --method threshold -t=-0.20,0.20 -o "$SAMPLE_DIR/${SAMPLE}.called.cns"

This is the result :

sample  | CHR   |   Start   |  END          |    Size (bp)   | log2_ratio  | cn   | Type_CNVs

Sample |chr20  | 168618 |58182109  |58013491     |0.115176    |1      |        loss