CNVKit 0.9.9 Batch mode has inconsistent CN and log2Ratio about cnvkit HOT 1 OPEN

Hi @JD12138,

The steps leading to sample.call.cns file are not vey well documented :

1. Raw log2ratios (the ones contained in your sample.cns file) are filtered to remove likely false-positive segments (based on confidence interval calculation)
2. Segments are median-centered and the "p_ttest" column is calculated (p-value of a t-test)
3. Eventually integer copy number values are called from log2ratio values (= "cn" column), using thresholds method with following thresholds : -1.1, -0.25, 0.2, 0.7

To sum up your observed CN and log2ratio values are not inconsistent
=> Everytime a log2ratio falls between -0.25 and 0.2, called CN is "neutral" = reference ploidy = 2 (by default)
=> Your first row with log2ratio=0.224267 is above 0.2 threshold so CN=3 is called

Hope this helped !
Have a nice day,
Felix.

from cnvkit.