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epi2me-labs / wf-somatic-variation

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Are there any future plans for a CNV module? #11

Open TBradley27 opened 9 months ago

TBradley27 commented 9 months ago

Is your feature related to a problem?

The ability to identify copy number variants from matched tumour and normal (i.e. non-tumour) samples having undergone whole genome sequencing with ONT sequencing platforms

Describe the solution you'd like

For a CNV caller to be integrated into the wf-somatic-variation pipeline which is specifically designed to work with long-read data, and also makes use of matched non-tumour/normals samples so that germline and somatic CNVs can be distinguished from each other

Describe alternatives you've considered

I have considered using the --cnv module with the wf-human-variation pipeline, which utilises QDNASeq but this does not exploit the additional information obtained from having a matched non-tumour sample.

Additional context

No response

RenzoTale88 commented 9 months ago

Hi @TBradley27, thank you for your question and interest in wf-somatic-variation! We are currently exploring this functionality to the workflow, although we are not in the position of give a timeline regarding it's implementation. I'll leave this issue open, and come back to notify you as soon as there will be updates in this regard.