Why cnvkit genemetrics command default threshold is 0.2?
1 answer
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.
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