Tajima'D and low-density SNP data

Question

[chrys.delord]

Dear all,

I am quite new to analysis of SNP data :-) My case is a bit particular because I only have genotypes from a few number of SNPs (~130) and more importantly, I do NOT have the associated DNA sequences because genotyping was performed through mass-spectrometry (and not sequencing!)

I was wondering if I still could use information from allele frequency spectrum and, for example, compute Tajima's D on my dataset?

Thank you very much for your enlightment!

Have a good day,

Chrys

Answer 1

[Kevin Blighe]

You could first extract sequence surround your SNPs, and there are various ways of doing this. There is a previous Biostars thread: extract sequence around snp

With the sequences, you then can create a DNAbin object using as.DNAbin() (from ape package) in R and run tajima.test() (from pegas package) on this. This will calculate Tajima's D.

[giulia.trauzzi]

Would that work if the SNPs are called de novo and not referenced-based??

[Kevin Blighe]

I am unsure / Non sono sicuro