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

'N' instead of a reference call #5

Open
JudithNeukamm opened this issue Jun 8, 2020 · 0 comments
Open

'N' instead of a reference call #5

JudithNeukamm opened this issue Jun 8, 2020 · 0 comments

Comments

@JudithNeukamm
Copy link

I recognized that in case of a reference call, MVCFA writes an 'N' in the alignment (SNP and complete genome). This only happens when using GATK3.8+. I fixed the corresponding lines in the code, however, did not test it systematically (but it seemed to have work for the analysis I did).
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
@JudithNeukamm