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Revive the cnvkit implementation for somatic copy number alteration calling #236

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ericblanc20 opened this issue Nov 7, 2022 · 0 comments

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@ericblanc20
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Is your feature request related to a problem? Please describe.
cnvkit is a superior alternative to copywriter for exome cases, and presumably also to Control_FREEC for whole genome cases.

Describe the solution you'd like
Clemens has implemented cnvkit in snappy, but this code hasn't been maintained. A new implementation also offers the possibility to create a panel of normals which could benefit the processing of smaller cohorts. The new implementation could also support whole genome data.

Describe alternatives you've considered
Clemens's code could perhaps be simply updated to work again with the current snappy version. We might loose the separation of the panel of normals, and perhaps also the generalisation for whole genome datasets.

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