[adegenet-forum] SNP positional information

Joanne Berghout, Miss joanne.berghout at mail.mcgill.ca
Wed Apr 14 01:22:19 CEST 2010

Hello adegenet users,

Is there a way that I can assign genetic positions to my SNPs?

I've just downloaded the ape, adegenet and pegas packages in R and I'm trying to analyze a data set of 400 individuals (13 populations) for 78 SNPs.

The data was collected by sequencing a single gene across each of the exons and looking for polymorphic sites both manually (chromatogram inspection) and using PhredPhrap.  I've been able up upload the data as a data frame (using read.loci) where each row is an individual and each column is a SNP (alleles coded as A/A).  I would like to look at the haplotype differences in the different populations, as well as do some neutrality tests (specifically Tajima's D) and a few other standard descriptive statistics.

I am trying to avoid creating FASTA files of the whole sequence for each of my individuals as I have multiple non-overlapping amplicons for each individual which (unless you also have a suggestion here) means that I would have to manually combine thousands of sequence reads (and edit for accuracy as PhredPhrap miscalled or just missed on quite a number of SNPs).


PS. I'm a pretty new R user, though I have a fair bit of experience with the R/qtl package as all my work so far has been on very straightforward inbred mouse crosses.  So, please, I would appreciate a little simplicity and explanation... 

More information about the adegenet-forum mailing list