Hello all,
I'm trying to calculate the pi and phi values for 3 different VCF files. I have attempted to download the packages VCFtools, DNAsp, and PopGenome for this. However, I've run into several problems. Neither VCFtools nor DNAsp are compatible with my version of R (version 4.0.3), and when I attempt to read in the vcf file using the readData command in PopGenome, I am met with a "cannot find path !" error. As of right now, my code line looks like this:
GENOME.class <- readData("VCF copies", format="VCF", gffpath="GFF")
I would like to be able to calculate pi and phi of these files on PopGenome. If I can't, though, which versions of R are compatible with VCFtools so that I might try to calculate these statistics there?
Thank you all very much. I'm pretty inexperienced with coding, so any help is greatly appreciated.
Have you found a solution to this yet? I am having the same issue!
"cannot find path