-
Notifications
You must be signed in to change notification settings - Fork 37
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
unsure how SNPgenie does the polarization of mutations #54
Comments
Greetings, Murillo! Thanks a lot for the question. Actually, being designed originally for πN/πS, SNPGenie is entirely phylogeny-agnostic. This mean it is not calculating dN/dS (or πN/πS) along branches or lineages, but rather simply the mean value between all choose(n,2) pairs of extant (provided) sequences. This may have less power than methods that trace changes over a phylogeny. On the other hand, the approach is robust to errors in phylogenetic and ancestral sequence reconstruction, and to artifacts due to linkage or recombination. Note that this distinction is probably only necessary for dN/dS, because πN/πS usually employs this non-phylogenetic by definition (i.e., it's a population measure). Let me know if that helps! |
Hi,
It's not clear to me how SNPgenie polarizes the mutations (to compute dN/dS and piN/piS).
Does it assume the ancestral states are the ones supplied in the reference fasta? If so, how would SNPgenie deal with having ancestral states in the reference fasta that do not mach the REF column in the VCF?
Thank you!
The text was updated successfully, but these errors were encountered: