plotting allele frequencies generated using vcftools

Question

[Dtriumph]

Hi,

I'm trying to plot allele frequency of my GBS data. I could generate the allele frequencies for each chromosome separately using vcftools and output files are in .frq format. I couldn't find a specific R package that help plot the data.

I appreciate any help with links to relevant R packages...

Thanks!

[porkbellydotcom]

Need the exact same thing. Did you ever solve this?

Answer 1

[venu]

If you would like to get an overview of the AF distribution, you can use simple density function from R. Something like following

# read data into R object (ex: dat)

plot(density(dat$AF)) #AF - field which contains AF values

[Dtriumph]

Thanks for your answer....