Chase W. Nelson 倪誠志

Hello @nicolo-tellini ! Thanks for the great questions. NONREF_NONPOLY means the major allele at the site does not match the reference sequence, and the site is not polymorphic. Thus, the...

Greetings, Chongli! That's a great question. First, we note that gene diversity (expected heterozygosity) at a nucleotide site as h=1-∑x^2, where x takes the frequency of every allele at the...

π is the mean pairwise divergence within a deeply sequenced sample. So, if that is what you want to determine, then it's correct. However, if you want to determine divergence...

Hello, Chongli! That really depends on your question. If you are calculating the statistic for each gene separately, you'd probably want to include it in each each. But if you're...

Greetings @passdan ! Apologies, as this script is brand new and not yet tested on the between-group output. I would be very happy to fix the bugs and update both...

Thanks again for your patience and for testing this out on the between group results! I have substantially updated the sliding window script for use with all three codon result...

Greetings, Peter! Thanks for the message. That sounds like a bad bug that should have raised a warning. I have not previously observed it. If you could provide a reproducible...

Thanks a lot for the question @annasimonsen! Unfortunately I wrote the script with chromosomes (not genes) in mind and did not have enough foresight to allow flexible usage without the...

Greetings, @aspitaleri! Thanks for the question and for using SNPGenie. The approach you describe does correspond to the "within-group" analysis. However, which approach to use depends on several factors, and...

Unfortunately, the VCF format depends on settings and I am not sure which format is output. There is example data in the example data directory, but it may or may...