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plotting allele frequencies generated using vcftools

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!

gwas genome plots snp vcftools
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updated by venu venu • written by Dtriumph • Dtriumph

1 answer

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
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written by venu venu

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