Vcf Tools For Fst

Question

[Tohamy]

Dear all, I used VCF tools to calculate Fst between two populations but now I need to calculate pairwise FST between 154 individuals within each population but I do not know how can I make this? Does anybody of you have idea how can I make this? I used this command to get Fst between the two populations:

HABIBA> vcftools --vcf adjusted_10varc30e0.vcf --weir-fst-pop TOHAMY_USDA --weir-fst-pop TOHAMY_IPK --out OUT

Thanks in advance and I am waiting your answers. Best regards, Tohamy

Answer 1

[Jorge Amigo]

Fst is a measurement of how genetically different 2 populations are. in fact, it's usually referred as the genetic distance among populations.

what you are trying to measure, or at least what I understand from your words, is not the differentiation inter-population, but intra-populations. we use a conceptually similar index to measure it, called Fs or local inbreeding, but I'm pretty sure you'll find very useful the "--relatedness" and the "--relatedness2" options from vcftools, which can give you an estimate of how the samples differ inside a particular population.

[Tohamy]

First of all, thanks for your help. Could you please write me the command line that I could use? Because it is my first time to use VCF tools Thanks again for all your help!

[Jorge Amigo]

as I said I haven't used it, but it should be something as simple as "vcftools --vcf yourvcffile --relatedness" if all your samples are contained in that multisample "yourvcffile" file. if not you may either merge them all into a single vcf file or probably add several "--vcf vcffile" strings (this last one I haven't tested it).

[Adrian Pelin]

Is there any way to calculate Fst from VCF files of polyploid organisms? VCFtools seems to give an error.

[Jorge Amigo]

the documentation says that VCFtools "aim to support polyploid data as well". in case you find any problem processing non diploid vcf files you should report that error to the VCFtools' development team.