8000 Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed · Issue #1054 · nf-core/eager · GitHub
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Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed #1054

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TCLamnidis opened this issue Feb 23, 2024 · 0 comments
Open

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

TCLamnidis opened this issue Feb 23, 2024 · 0 comments
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@TCLamnidis
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See stschiff/sequenceTools#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?
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