Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
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
Labels
DSL2

Comments

@TCLamnidis
Copy link
Collaborator

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?
TCLamnidis added a commit that referenced this issue Mar 8, 2024
@TCLamnidis
remove todo about issue #1054
61df8b9
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
DSL2
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@TCLamnidis