-
Notifications
You must be signed in to change notification settings - Fork 18
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
QUESTION: Hetero sites. #53
Comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi there,
I just have a question regarding on how the aligner will deal with sites where there are just two reads spawning the reference marker gene with some level of contamination. In other words, I'm not sure how the alignment proceeds when there are two different bases (heterogeneity) in the same position. Will the aligner pick up a random one or ignore the site and add a ?/N sign?
The same question can also cover similar situations, such in the cases where there are 3 reads and one of them contains contaminated bases or just sequencing errors. I guess the best way will be to set up a higher coverage threshold but if that's not possible then I would like to know how the aligner behaves on this cases.
Any help or guidance will be much appreciated!
The text was updated successfully, but these errors were encountered: