These are chat archives for dereneaton/ipyrad

2nd
Apr 2017
Isaac Overcast
@isaacovercast
Apr 02 2017 13:03
@natagalle How many is many? What constitutes normal is really organism dependent. If diversity is low, then maybe this wouldn't be too surprising. If you use basically any of the output except the .loci format then these loci will be automatically filtered because they don't contain any variation. Are you trying to use the .loci file for downstream analysis?
To answer your question, there isn't a baked in way to remove monomorphic loci.
natagalle
@natagalle
Apr 02 2017 16:49
@isaacovercast Thank you very much for your reply. I am indeed working with an endangered species that has very low genetic variability, but I wasn't sure if what I found is related to my organism or if did something wrong in my analysis. I was actually working with the .vcf file when I noticed this. I estimated the per site nucleotide diversity (pi) and noticed that from 32,123 sites, 91% had pi=0. I checked the genotypes of all my individuals in some of these sites and confirmed that they were all the same. So that's why I was confused, because I thought the .vcf file contained only the polymorphic loci.