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nf-core

Hi ! I have used the pipeline in wgts mode with donor samples and it works really well, thank you ! I tried to use it in targeted mode but it doesn't accept donor samples. Is there a restriction in the tools that accept donor samples in wgts (sage and amber if I understood well), and can't anymore in targeted mode ? In brief is it just not implemented in the pipeline (and could be in the future) or is it not implemented in the tools themselves ?

hi <@U0AF61PN90Q> just clarifying with "donor material" you mean healthy material (blood/tissue) or the tumour?  i.e. the default configurations for most targeted uses 'tumor only' so it could be that the configs for targeted tumor+normal isn't quite optimal/configured, the underlying tools should be able to handle it just fine. After you confirm exactly how you're trying to run it I'll try to loop in the person most likely having run it in that mode

Thanks ! Sorry I meant donor from a bone marrow transplant for example, to substract variants (<https://nf-co.re/oncoanalyser/2.3.0/docs/usage#paired-tumor-and-normal-dna-with-donor-sample|nf-co.re/oncoanalyser/2.3.0/docs/usage#…>)

For the moment I'm running it with only tumor+normal, it seems that at least this configuration works !

Ah check, I will have to check with the dev team is this is a feature supported in targeted <@U09F8TB2QGK> can you chime in?

Hi <@U0AF61PN90Q>, if you need tumor+donor mode, using tumor+normal mode as you suggested is fine. Under the hood, the normal and donor samples are just passed as comma separated 'reference' samples to Sage and Amber, see:
<https://github.com/nf-core/oncoanalyser/blob/3.0.0-rc.5/modules/local/sage/somatic/main.nf#L41-L44|github.com/nf-core/oncoanalyser/blob/…/main.nf#…>

Tumor+normal+donor isn't supported, though this was more an oversight in the pre-run checks and should be supported. The eventual plan is to allow multiple normal samples e.g. tumor+normal1+normal2+etc and drop the donor sample category, but this requires a bigger change (aiming for OA v3.1, or possibility later versions)

Thank you for the quick answer and the code, really nice to understand how the "donor" samples are used in Sage and Amber.
What is the difference in targeted that is preventing to use a second reference in Sage and Amber ? Because I'd like to use tumor+normal+donor.

Theoretically, if I removed these lines : <https://github.com/nf-core/oncoanalyser/blob/50c177c36b977c6f2f8b5c4375d3e6ddaf40e3d0/lib/Utils.groovy#L402-L407|github.com/nf-core/oncoanalyser/blob/…/Utils.groovy#…> it would run in targeted with tumor + normal + donor ? But there might other problems.

Otherwise, at least for sage outputs I could filter manually the variants found in the donor in tumor only.

I’ll leave Luan to answer your question, but wanted to add that donor in targeted mode was intentionally disallowed in the 0.5.0 release

The need for that particular analysis scenario just hadn’t been revisited since (so thanks for bringing to our attention)

> Theoretically, if I removed these lines : <https://github.com/nf-core/oncoanalyser/blob/50c177c36b977c6f2f8b5c4375d3e6ddaf40e3d0/lib/Utils.groovy#L402-L407|github.com/nf-core/oncoanalyser/blob/…/Utils.groovy#…> it would run in targeted with tumor + normal + donor ?
You could remove those lines yes :slightly_smiling_face:. This is what we will at least do for the OA 3.1 release

Thanks everyone, I will try that for now !