Question: Why cnvkit genemetrics command default threshold is 0.2?
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gravatar for MatthewP
11 months ago by
MatthewP390
China
MatthewP390 wrote:

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?

cnvkit • 315 views
ADD COMMENTlink modified 11 months ago by ATpoint31k • written 11 months ago by MatthewP390
2
gravatar for ATpoint
11 months ago by
ATpoint31k
Germany
ATpoint31k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint31k
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