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?
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vctrm67 •
1 answer
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.
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