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Is joint genotyping suitable for clinical purposes?

thedamthedam BarcelonaMember

I've seen a lot of recommendations and benefits why should I use joint genotyping but still I didn't find a clear answer if it's indeed suitable for clinical applications.

I have to analyse ~20 WES samples per week - these are patients data with various diseases. So for sure I'll have a patient that has an unique variant (singleton) across all my data. Having this knowledge, is it safe to use joint genotyping? According to the description in "Why should I use joint calling for germline short variants?" my singletons may be lost...
So in my case, should I use it or not?

Thank you for any clarifications!

Regards
DL

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