-
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
Using SNPGenie on VCF from RAD-seq #68
Comments
Dear Aude, apologies that I missed this. Unfortunately I've never known anyone to use SNPGenie for RAD-seq data but in principle if you have a VCF file it should be possible. However, indeed, you'd need a reference FASTA; the site numbers in the VCF would need to correspond to the coordinates of that FASTA; and you'd need a GTF specifying any genes therein. Depending on your starting data, this may require quite a bit of manual/scripting preparation. Let me know if this helps. Chase |
Dear developper,
I'm interested in estimating piN/piS for 6 populations of individuals. The individuals were sequenced separately in RAD-seq, the reads mapped on the reference genome and then the variant calling was made via Stacks which gives me a VCF (format 1). I read the part of the manual explaining how to use SNPGenie with VCF format, and I'm still not quite sure I undestand how to use it.
First, can SNPGenie be run on several individuals at the same time ? Or should I run it on one individual at the time and then average the piN/piS per population?
Second, I see that even using the VCF format, I need to provide a fasta file, but I'm not sure how to obtain this fasta... I only have the fasta of the reads per individuals. Could you please explain what type of fasta I need ?
Thank you,
Aude
The text was updated successfully, but these errors were encountered: