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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Why adding a pseudocount of flat reference to the aggregated reference? #845

Open 28rietd opened 9 months ago

28rietd commented 9 months ago

Can you explain what the reason is for adding a flat reference to the aggregated reference (see https://github.com/etal/cnvkit/blob/e119e87389e7335d1f98944b97f7f7068f5a7244/cnvlib/reference.py#L293C1-L293C37)? In case of CNV calling with only a single normal sample it seems that this flat reference will get a lot of weight.