Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed

nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

https://nf-co.re/eager

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Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed #1054

Open TCLamnidis opened 7 months ago

TCLamnidis commented 7 months ago

See https://github.com/stschiff/sequenceTools/issues/24

In cases where PE un-collapsed reads from a single-stranded library are used in pileupcaller, the damage model is off, and damage artefacts will still make it into the genotypes.

Maybe we should throw a warning when a user specifies pileupcaller as the genotyper while also opting to --skip_collapse?