Question: the function of readVCF in PopGenome R package
gravatar for mike229lin
14 months ago by
mike229lin10 wrote:


I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during the protocol

First, I want to analyze whole genome level data. In the manual of PopGenome, it says I should input a specific chromosome or scaffold name. If I want to generate Fst of whole genome, what should I input? The function of read data seems unavailable for me after I tried many times using the function .

Second, how can I set the "numcol" column if I have 1.7*10E7 SNP sites in my data?

I have about 7000 scaffolds in my reference genome, it seems I should write a R script to make PopGenome package calculate Fst ?

fst popgenome R vcf • 578 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 14 months ago by mike229lin10
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