CNVKit interpretation of results?

Question

[vctrm67]

I am wondering how to best interpret the output of CNVKit calling that I couldn't really find on the website. I have these data in the .call.cns file:

chromosome      start   end     gene    log2    baf     cn      cn1     cn2     depth   probes  weight
chr1    10500   121484934       TNFRSF14,ERRFI1,MTOR,SPEN,SDHB,ARID1A,MYCL,MPL,MUTYH,CDKN2C,JUN,JAK1,FUBP1,NRAS,FAM46C,HSD3B1,NOTCH2    0.356172        0.469546        3       2       1       57.2836 1056    127.64`
...

What exactly does "depth" refer to? Is this the average coverage depth for all CNVs listed in the base range? This seems implausible because I see values like "0.00523127" for some ranges, which seems wrong. Or is it a logged coverage?

Answer 1

[jared.andrews07]

From the docs:

For .cnn sample-specific files:

The depth column is the robust average of absolute-scale coverage depths from the input .cnn files, but without any bias corrections.

For .cns segment files:

The depth and log2 is the weighted mean of the input bin-level values corresponding to the segment.