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

Determine genotype call from PL field in VCF files #13

Open
carolyncaron opened this issue Apr 28, 2017 · 0 comments
Open

Determine genotype call from PL field in VCF files #13

carolyncaron opened this issue Apr 28, 2017 · 0 comments
Assignees
@carolyncaron
Labels
enhancement

Comments

@carolyncaron
Copy link
Member

Currently, the genotype call is interpreted from the GT field, which is not always reflective of the PL field. GT is determined somewhat based on Hardy-Weinburg, which does not apply to our populations.

Though this is the ideal approach for our own group, I can't help but wonder about other prospective users of the loader. Is using PL a generic approach? Or will other groups want to load genotypes solely based on GT? Should we make it an option?
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@carolyncaron carolyncaron

Labels
enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@carolyncaron