How to read a .vcf file in R

[mara...@gmail.com]

Hi, dDocent team! Please, could someone tell me how to read a vcf file in R to calculate basic population genetics statistics? I have tried several options without success.
In advance thanks,
M.

[Sophie D]

Hi,

you could try with this package: vcfR (10.1111/1755-0998.12549). I personally I have no experience yet with it as I just discovered this package this week! What packages did you try so far?

Greetings,

Sophie

--

Sophie Delerue-Ricard, PhD student in Marine Molecular Evolutionary Ecology, Belgium

Leuven University & Institute for Agricultural and Fisheries Research

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[mara...@gmail.com]

Hi Sophie,

Yes, I have tested with this R package, but have the problem that vcfR package does not recognize my .vcf files, I have tried to read my file and also other files from the examples folder of vcftools and I get this error:

> myvcf<-read.vcfR(annotate-test.vcf)
Error in path.expand(file) : object 'annotate' not found

> myvcf<-read.vcfR(popaus03.vcf, nrows= 2056, skip=0, convertNA=TRUE, verbose=TRUE)
Error in path.expand(file) : object 'popaus03.vcf' not found.

Some idea?

Thanks,
M.

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[Joel Anderson]

You might try the linux version of the software PGDSpider http://www.cmpg.unibe.ch/software/PGDSpider/
This can read a .vcf file and convert it to several formats that are more useable for traditional popgen programs.  I'm sure one of those formats (Genepop, for instance) could be read into R.

[rsp...@gmail.com]

On Tuesday, November 7, 2017 at 2:57:58 PM UTC-6, mara...@gmail.com wrote:

I'm sure the original questioner has found a solution by now!! But for those who may come along later, there's vcf2genind if the plan is to use adegenet.

PGDSpider does work well as Joel mentioned.