Why cnvkit genemetrics command default threshold is 0.2?

Question

[MatthewP]

Hello, cnvkit genemetrics command's default threshold is 0.2(pure tumor sample), this will report single-copy gains and losses. However log2 ratio means 1.1487 times than reference ploidy, not 1.5. Why?

Answer 1

[ATpoint]

Because 1.5 being 3 copies when 2 are expected for a diploid genome (3/2=1.5) assume a perfectly homogeneous sample (= there are no clonal sub-populations that do or do not have the CNV) with only a single gain and no contaminations by normal DNA. A lower threshold accounts for samples never being fulfilling the above criteria. Please read the docs.