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

Can I get compy number between white blood cell bam and adjacent normal tissue bam #919

Open
shenhaizhongdechanrao opened this issue Oct 3, 2024 · 1 comment
Open

Can I get compy number between white blood cell bam and adjacent normal tissue bam #919

shenhaizhongdechanrao opened this issue Oct 3, 2024 · 1 comment
Labels
question

Comments

@shenhaizhongdechanrao
Copy link

hi, Can I get compy number between white blood cell bam and adjacent normal tissue bam. Is it suitable for samples between non-tumors?
@etal
Copy link
Owner

etal commented Nov 13, 2024

Could work, depending on the cancer. Is this leukemia/lymphoma?

If you're not sure about your "normal" samples, you could try running CNVkit with a "flat" reference on those samples to see if they have any recurrent, large-scale copy number alterations. If they do, you can omit those samples or overwrite the altered regions with a log2 value of 0.0.

@etal etal added the question label Nov 13, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
question
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@etal @shenhaizhongdechanrao