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Revamp somatic CNV calling #535

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ericblanc20 opened this issue Jul 25, 2024 · 0 comments · May be fixed by #558
Open

Revamp somatic CNV calling #535

ericblanc20 opened this issue Jul 25, 2024 · 0 comments · May be fixed by #558

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@ericblanc20
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Is your feature request related to a problem? Please describe.

  • There are separate steps for WGS & WES CNV calling, it should be unnecessary.
  • The WGS branch has not kept up with progress in the rest of the pipeline
  • It is a good playground to test new ideas for the overall pipeline architecture

Describe the solution you'd like

  • Clear, easy to understand code
  • Support for WES & WGS (& panel data?)
  • Support for flat and panel of normals priors, as well as nromal/tumor pairs
  • Support for cnvkit, purecn & sequenza (WES), cnvkit & possibly Control_FREEC for WGS
  • Support for germline & somatic variants
  • Support for purity (using ASCAT, Theta2/Hatchet or others)

Describe alternatives you've considered
Just updating somatic_wgs_cnv_calling.
@ericblanc20 ericblanc20 linked a pull request Dec 6, 2024 that will close this issue
feat: revamp somatic cnv calling #558
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feat: revamp somatic cnv calling bihealth/snappy-pipeline
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@ericblanc20