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.

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

Add coverage and insert size plots #91

Open
sorelfitzgibbon opened this issue Jan 10, 2025 · 1 comment
Open

Add coverage and insert size plots #91

sorelfitzgibbon opened this issue Jan 10, 2025 · 1 comment
Assignees

Comments

@sorelfitzgibbon
Copy link
Collaborator

Probably both from SAMtools stats output

@sorelfitzgibbon sorelfitzgibbon self-assigned this Jan 10, 2025
@sorelfitzgibbon
Copy link
Collaborator Author

sorelfitzgibbon commented Jan 14, 2025

@yashpatel6 @tyamaguchi-ucla
For this issue:

  • For generate-SQC-BAM I propose to use plot-bamstats which is part of the SAMtools package to create sample level BAM QC plots from the SAMtools stats output. Here are the default plots for a single PCAWG sample:
    plots-bamstats-pcawg63.pdf.
    This requires adding gnuplot to the SAMtools docker, which Claude estimated would only add 5-10 MB out of 100-200 MB for SAMtools alone.
  • For the generate-CQC-BAM I propose using the scripts currently in tool-QC-script to generate these cohort level plots from both the SAMtools stats and Picard CollectWGSmetrics outputs.
    plots-cohort-pcawg63.pdf

In both cases each plot would be created as an individual file, unless we add a step to concatenate them.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant