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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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I couldn't understand how to caculate log2 ratio for bins just reading the CNVkit documentation ,who knows can reply me ? #704

Open whiffen-cann opened 2 years ago

jasmoonli commented 2 years ago

According to the documentary,

The log2 coverage depth is the robust average of coverage depths, excluding extreme outliers, observed at the corresponding bin in each the sample .cnn files used to construct the reference.

You can calculate it by log2（copy number/2）. For instance, when the copy number equals to 2, you get log2 ratio log2(2/2) = log2(1) = 0. When the copy number equals to 3, you get log2 ratio log2(3/2) = log2(1.5) =0.5849625.

whiffen-cann commented 2 years ago

According to the documentary,

The log2 coverage depth is the robust average of coverage depths, excluding extreme outliers, observed at the corresponding bin in each the sample .cnn files used to construct the reference.

You can calculate it by log2（copy number/2）. For instance, when the copy number equals to 2, you get log2 ratio log2(2/2) = log2(1) = 0. When the copy number equals to 3, you get log2 ratio log2(3/2) = log2(1.5) =0.5849625.

Thanks for your reply very much ,your example makes it easy for me to understand.