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

Update VQSR commands to follow recent GATK best practices #133

Open
tyamaguchi-ucla opened this issue Jun 1, 2023 · 0 comments
Open

Update VQSR commands to follow recent GATK best practices #133

tyamaguchi-ucla opened this issue Jun 1, 2023 · 0 comments

Comments

@tyamaguchi-ucla
Copy link

It looks like they have updated the VQSR models.

https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

Also, for WXS samples, we may want to remove the DP from the model as suggested here.
https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR-
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@tyamaguchi-ucla