Greetings!
I am dealing with NGS data. I have a vcf file of the called SNPs. I want to do population diversity and differentiation analysis with it but unfortunately, I unable to do so though I have tried using different software too. Can anyone help me in suggesting ways to do analysis using the vcf file?
Hi Gargee,
There are multiple ways of calculating Fst using a vcf file. The easiest way is to use Vcftools, it gives you fst based on Wier and Cockerham estimation.
If you are interested in pairwise Fst to look at population differentiation, you can also use R packages like Heifstat. But for that, you need to extract the genotypes from your VCf to an r readable file .csv or .txt.
Hi Abhinav
I would not use Vcftools as it has issues with handling missing data and I noticed different results when comparing nucleotidic diversities with other softwares. I would suggest to use PopGenome under which is a very powerfull software under R. An alternative is the SNPrelate package (from Bioconductor) also under R. Both packages can offer Fst estimation from genotypic data in a vcf file format.
Good luck.
Jean-Luc
you may want to follow this simple tutorial: https://speciationgenomics.github.io/per_site_Fst/
- Badges
- Science method